rs3763463

Variant names:

• chr7-108457047-C-G
• rs3763463

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 0.0942 in 151,734 control chromosomes in the GnomAD database, including 714 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 0.094 (714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 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: 0.0942 AC: 14289 AN: 151618 Hom.: 714 Cov.: 31

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0878

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0942 AC: 14293 AN: 151734 Hom.: 714 Cov.: 31 AF XY: 0.0960 AC XY: 7112 AN XY: 74108

African (AFR) AF: 0.0744 AC: 3080 AN: 41374

American (AMR) AF: 0.0876 AC: 1338 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3470

East Asian (EAS) AF: 0.0590 AC: 303 AN: 5136

South Asian (SAS) AF: 0.0887 AC: 425 AN: 4790

European-Finnish (FIN) AF: 0.151 AC: 1574 AN: 10446

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7059 AN: 67940

Other (OTH) AF: 0.0966 AC: 203 AN: 2102

Alfa AF: 0.0950 Hom.: 87

Bravo AF: 0.0875

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.95
PromoterAI		0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3763463; hg19: chr7-108097491;