rs929731

Variant names:

• chr7-131630333-G-A
• rs929731

Your query was ambiguous. Multiple possible variants found:

• chr7-131630333-G-A
• chr7-131630333-G-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 0.477 in 152,098 control chromosomes in the GnomAD database, including 21,639 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 0.48 (21639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.477 AC: 72514 AN: 151980 Hom.: 21643 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72495 AN: 152098 Hom.: 21639 Cov.: 32 AF XY: 0.470 AC XY: 34954 AN XY: 74346

African (AFR) AF: 0.132 AC: 5488 AN: 41516

American (AMR) AF: 0.523 AC: 7996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3470

East Asian (EAS) AF: 0.181 AC: 931 AN: 5154

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4820

European-Finnish (FIN) AF: 0.605 AC: 6392 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46140 AN: 67958

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.605 Hom.: 91683

Bravo AF: 0.457

Asia WGS AF: 0.235 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.43
DANN	Benign	0.65
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs929731; hg19: chr7-131315092; COSMIC: COSV107155545;