rs7632500

Variant names:

• chr3-168007561-A-G
• rs7632500

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 0.166 in 152,120 control chromosomes in the GnomAD database, including 4,296 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 0.17 (4296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.166 AC: 25186 AN: 152002 Hom.: 4282 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.166 AC: 25253 AN: 152120 Hom.: 4296 Cov.: 32 AF XY: 0.163 AC XY: 12116 AN XY: 74398

African (AFR) AF: 0.433 AC: 17927 AN: 41400

American (AMR) AF: 0.175 AC: 2677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.112 AC: 579 AN: 5182

South Asian (SAS) AF: 0.0399 AC: 192 AN: 4818

European-Finnish (FIN) AF: 0.0282 AC: 300 AN: 10620

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0449 AC: 3051 AN: 68014

Other (OTH) AF: 0.144 AC: 304 AN: 2116

Alfa AF: 0.0900 Hom.: 2801

Bravo AF: 0.191

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7632500; hg19: chr3-167725349;