Question for rs1802963

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Nathalie Gaudreault

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Jul 22, 2024, 2:37:54 PM (3 days ago) Jul 22
to gen...@soe.ucsc.edu

Good day

 

We are actively working on SERPINA1 gene and its variants

I would like to know why rs1802963 was G/T in dbSNP 151 and older, and was changed to C/G in dbSNP 153 and dbSNP155 ?

 

What was the reason supporting the change ?

Was the information in build 151 and older wrong ?

 

This change has a big implication on the protein, Stop_gained versus missense variant

Thanks for your support

 

SERPINA1 (NM_000295): stop_gained E (GAA) --> * (TAA)

GENCODE V46  

SERPINA1 (ENST00000393088.8) 

missense_variant E (GAA) --> Q (CAA)

 

 

 

Nathalie Gaudreault

Research Professional

Laboratory of Yohan Bossé

 

Centre de Recherche

Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ)

2725, chemin Sainte-Foy, Room A-2017
Quebec (Quebec) Canada
G1V 4G5

Tel : 418-656-8711 ext : 3382

nathalie....@criucpq.ulaval.ca

yohanbosselab.com

 

Logo_IUCPQ_Recherche_coul_hor

 

Angie Hinrichs

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Jul 22, 2024, 4:16:44 PM (3 days ago) Jul 22
to Nathalie Gaudreault, gen...@soe.ucsc.edu, snp-...@ncbi.nlm.nih.gov
Hi Nathalie,

That is a very interesting observation, but since the UCSC Genome Browser merely displays data that we download from dbSNP, we can't determine why the alleles of rs1802963 changed between builds 151 and 153.  So I am passing along your question to dbSNP by Cc: snp-...@ncbi.nlm.nih.gov .

To the dbSNP team: currently https://www.ncbi.nlm.nih.gov/snp/rs1802963#submissions shows a single submission for rs1802963, ClinVar variant RCV000508718.1, with genomic alleles C/G.  However, the build 151 database-dump download file SubSNP.bcp.gz shows that it was based on submitted SNP ss2423541, with genomic alleles C/A.  I would have expected the info from ss2423541 and RCV000508718.1 to have been merged when RCV000508718.1 was added to rs1802963 (C/A/G), but it looks like ss2423541 was dropped -- any idea why?  

This is the relevant row from the b151 SubSNP table:

subsnp_id                     2423541
known_snp_handle              
known_snp_loc_id              
known_snp_loc_id_upp          
batch_id                      3308
loc_snp_id                    SNP000010747
loc_snp_id_upp                SNP000010747
synonym_names                
loc_sts_id                    
loc_sts_id_upp                
segregate                     ?
indiv_homozygosity_detected   ?
PCR_confirmed_ind             ?
gene_name                    
sequence_len                  51
samplesize                    0
EXPRESSED_SEQUENCE_ind        ?
SOMATIC_ind                   ?
sub_locus_id                  0
create_time                   2000-11-07 13:36:00.0
last_updated_time             2003-10-10 19:10:00.0
ancestral_allele              
CpG_code                      1
variation_id                  17
top_or_bot_strand             B
validation_status             0
snp_id                        1802963
tax_id                        9606
chr_id                        28

Thanks,
Angie


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Angie Hinrichs, Bioinformatics Programmer
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