rs7638995

Variant names:

• chr3-69124224-C-A
• rs7638995

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 0.306 in 152,112 control chromosomes in the GnomAD database, including 9,955 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 0.31 (9955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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: 0.305 AC: 46393 AN: 151994 Hom.: 9918 Cov.: 33

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.306 AC: 46477 AN: 152112 Hom.: 9955 Cov.: 33 AF XY: 0.306 AC XY: 22726 AN XY: 74362

African (AFR) AF: 0.606 AC: 25122 AN: 41478

American (AMR) AF: 0.244 AC: 3726 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5172

South Asian (SAS) AF: 0.293 AC: 1418 AN: 4832

European-Finnish (FIN) AF: 0.154 AC: 1627 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11261 AN: 67990

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.247 Hom.: 1021

Bravo AF: 0.326

Asia WGS AF: 0.311 AC: 1084 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs7638995; hg19: chr3-69173375;