rs3763463

Positions:

• chr7-108457047-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.0876

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0590

Gnomad4 SAS AF: 0.0887

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0966

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763463; hg19: chr7-108097491;