rs4947510

Variant names:

• chr7-50457722-A-G
• rs4947510

Your query was ambiguous. Multiple possible variants found:

• chr7-50457722-A-G
• chr7-50457722-A-T

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 0.664 in 152,132 control chromosomes in the GnomAD database, including 33,982 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 0.66 (33982 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100977 AN: 152014 Hom.: 33955 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.664 AC: 101053 AN: 152132 Hom.: 33982 Cov.: 34 AF XY: 0.661 AC XY: 49185 AN XY: 74366

African (AFR) AF: 0.584 AC: 24244 AN: 41502

American (AMR) AF: 0.734 AC: 11235 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 2607 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2582 AN: 5160

South Asian (SAS) AF: 0.604 AC: 2906 AN: 4814

European-Finnish (FIN) AF: 0.639 AC: 6767 AN: 10582

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48372 AN: 67984

Other (OTH) AF: 0.688 AC: 1456 AN: 2116

Alfa AF: 0.706 Hom.: 64035

Bravo AF: 0.668

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.4
DANN	Benign	0.54
PhyloP100		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4947510; hg19: chr7-50525420; COSMIC: COSV63568086; COSMIC: COSV63568086;