rs7624691

Variant names:

• chr3-137144237-T-C
• rs7624691

Your query was ambiguous. Multiple possible variants found:

• chr3-137144237-T-C
• chr3-137144237-T-G

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 152,072 control chromosomes in the GnomAD database, including 18,789 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 (18789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74577 AN: 151954 Hom.: 18769 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.491 AC: 74642 AN: 152072 Hom.: 18789 Cov.: 32 AF XY: 0.494 AC XY: 36732 AN XY: 74344

African (AFR) AF: 0.588 AC: 24417 AN: 41492

American (AMR) AF: 0.497 AC: 7597 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2906 AN: 5174

South Asian (SAS) AF: 0.535 AC: 2582 AN: 4824

European-Finnish (FIN) AF: 0.451 AC: 4767 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29102 AN: 67964

Other (OTH) AF: 0.510 AC: 1075 AN: 2108

Alfa AF: 0.446 Hom.: 62572

Bravo AF: 0.498

Asia WGS AF: 0.560 AC: 1944 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7624691; hg19: chr3-136863079;