Re: [hgvs-discuss] reference genome for minus strand is not revese_complemented

[Reece Hart]

Sue-

It appears to me that the input variant is bogus and that the hgvs package wouldn't let you execute c_to_g. Here's what I see:

snafu$ hgvs-shell 
############################################################################
hgvs-shell -- interactive hgvs
hgvs version: 1.3.1.dev0+g83cde96.d20190515
data provider url: postgresql://anonymous:anonymous@localhost/uta_dev/uta_20170707
schema_version: 1.1
data_version: uta_20170707
sequences source: SeqRepo (/usr/local/share/seqrepo/latest)

>>> vc = hp.parse("NM_181714.3:c.4105_4117dupGCACTATGACTCT")
>>> seq = hdp.seqfetcher.fetch_seq(vc.ac)
>>> ti = hdp.get_tx_identity_info(vc.ac)
>>> len(seq)
4729
>>> %pprint
Pretty printing has been turned ON
>>> dict(ti)
{'tx_ac': 'NM_181714.3',
 'alt_ac': 'NM_181714.3',
 'alt_aln_method': 'transcript',
 'cds_start_i': 612,
 'cds_end_i': 2706,
 'lengths': [315, 106, 381, 530, 138, 97, 143, 133, 2876],
 'hgnc': 'LCA5'}
>>> vn = am38.c_to_g(vc)
...
HGVSInvalidIntervalError: The given coordinate is outside the bounds of the reference sequence.

CDS start and end are 613 (612 interbase) and 2706, so the CDS length is 2706-612=2094. 

Would you please construct a simple demonstration with code, generated roughly like the above?

-Reece

On Tue, Oct 29, 2019 at 5:30 PM Sue S <sues...@gmail.com> wrote:

Hello,

when I convert c_to_g for variant "NM_181714.3:c.4105_4117dupGCACTATGACTCT", the expected genomic variant is "NC_000006.11:g.80194698_80194710dupGCACTATGACTCT". It's on the minus strand, but the deleted sequences on the reference is not reverse complemented.

It should have been "NC_000006.11:g.80194698_80194710delAGAGTCATAGTGC" I believe? Does anyone know if it's not being done anymore? 

Thank you very much!

--
You received this message because you are subscribed to the Google Groups "hgvs-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hgvs-discuss...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hgvs-discuss/7da2aea7-cbd1-4929-977a-0d9da620b2ee%40googlegroups.com.

[Sue S]

Thanks very much for your kind reply Mr.Hart.

I repeated your steps and got the same result. I'm new to hgvs, I'd like to know how can you tell it is a bogus variant? from the CDS_start and end (4104_4117) compared to the actual CDS_start and end (612 to 2706)?

Regards,

To unsubscribe from this group and stop receiving emails from it, send an email to hgvs-d...@googlegroups.com.

[Reece Hart]

You're welcome.

The CDS length is 2094, so valid c. coordinates are 1-2094 (inclusive, 1-based). Your variant has c. positions far beyond that value.

-Reece 

To unsubscribe from this group and stop receiving emails from it, send an email to hgvs-discuss...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/hgvs-discuss/40e462cd-6037-4351-916c-535b38aec0f2%40googlegroups.com.