rs7731657

Variant names:

• chr5-130607626-T-C
• rs7731657

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 0.236 in 152,126 control chromosomes in the GnomAD database, including 4,505 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 0.24 (4505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.236 AC: 35872 AN: 152008 Hom.: 4486 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.236 AC: 35932 AN: 152126 Hom.: 4505 Cov.: 32 AF XY: 0.243 AC XY: 18081 AN XY: 74374

African (AFR) AF: 0.238 AC: 9880 AN: 41504

American (AMR) AF: 0.322 AC: 4924 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2067 AN: 5164

South Asian (SAS) AF: 0.253 AC: 1220 AN: 4830

European-Finnish (FIN) AF: 0.283 AC: 2999 AN: 10582

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13623 AN: 67990

Other (OTH) AF: 0.214 AC: 452 AN: 2108

Alfa AF: 0.211 Hom.: 10050

Bravo AF: 0.240

Asia WGS AF: 0.346 AC: 1202 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.0
DANN	Benign	0.80
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs7731657; hg19: chr5-129943319;