het FANCA del ex 15-22

Maria Kurnikova

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Apr 30, 2026, 4:43:42 PMApr 30

to HGVS Nomenclature

Dear HGVS Experts,

NGS targeted panel analysis revealed a heterozygous deletion of exons 15-22 in FANCA (reduced coverage in IGV and in silico analysis). Could you please clarify if, in this case, we can describe the deletion at the genomic level (prior to MLPA confirmation):

NC_000016.10:g.(?_89773271)_(89784964_?)del

where 89773271 is the position of the last nucleotide of exon 22, and 89784964 is the position of the first nucleotide of exon 15,

or only at the cDNA level:

FANCA(NM_000135.4):c.(1359+1_1360-1)_(2014+1_2015-1)del

where (1359+1_1360-1) are the boundaries of intron 14, and (2014+1_2015-1) are the boundaries of intron 22.

Kind regards,

Maria.

Johan den Dunnen

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May 1, 2026, 2:48:32 AMMay 1

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Dear Maria,

following HGVS nomenclature, the variant should be described as NC_000016.10:g.(89771815_89773270)_(89784965_89791402)del NM_000135.4:c.(1359+1_1360-1)_(2014+1_2015-1)del.

Note the format FANCA(NM_000135.4):c. is not correct, HGVS nomenclature does not allow the use of gene symbols in variant descriptions. Regarding NC_000016.10:g.(?_89773271)_(89784964_?)del, while you know the flanking exons (14 and 23) are not deleted, this information is missing in the description; you use a "?" indicating you have no information regarding where the deletion ends while you do have this information.

Best regards,

Johan den Dunnen
HUGO HGVS Variant Nomenclature Committee (HVNC)

Op donderdag 30 april 2026 om 22:43:42 UTC+2 schreef Maria Kurnikova:

Maria Kurnikova

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May 4, 2026, 9:34:05 AMMay 4

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Dear Professor Johan den Dunnen,

Thank you very much for your prompt response and clear explanations.

If I may, one more clarification: would the notation for this deletion change if panel sequencing followed by IGV analysis reveals a complete absence of coverage across exons 15–22, suggesting homozygosity?

Best regards,

Maria.

пятница, 1 мая 2026 г. в 09:48:32 UTC+3, jtden...@gmail.com:

Johan den Dunnen

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May 4, 2026, 10:46:36 AMMay 4

to HGVS Nomenclature

Dear Maria,

yes, when the variant was identified in homozygosity, following HGVS nomenclature "Alleles" (https://hgvs-nomenclature.org/stable/recommendations/DNA/alleles/) the variant description becomes NC_000016.10:g.[(89771815_89773270)_(89784965_89791402)del];[(89771815_89773270)_(89784965_89791402)del] NM_000135.4:c.[(1359+1_1360-1)_(2014+1_2015-1)del];[(1359+1_1360-1)_(2014+1_2015-1)del].