rs3763317

Variant names:

• chr6-32409011-C-T
• rs3763317

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.491 in 151,898 control chromosomes in the GnomAD database, including 18,620 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18620 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74487 AN: 151780 Hom.: 18606 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.490

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.491 AC: 74537 AN: 151898 Hom.: 18620 Cov.: 31 AF XY: 0.499 AC XY: 37015 AN XY: 74238

African (AFR) AF: 0.524 AC: 21699 AN: 41386

American (AMR) AF: 0.478 AC: 7293 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1820 AN: 3466

East Asian (EAS) AF: 0.627 AC: 3231 AN: 5152

South Asian (SAS) AF: 0.623 AC: 3003 AN: 4824

European-Finnish (FIN) AF: 0.543 AC: 5729 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30035 AN: 67930

Other (OTH) AF: 0.487 AC: 1030 AN: 2114

Alfa AF: 0.461 Hom.: 35960

Bravo AF: 0.490

Asia WGS AF: 0.606 AC: 2110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.21
PhyloP100		0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3763317; hg19: chr6-32376788;