rs7629693

Variant names:

• chr3-15367319-G-C
• rs7629693

Your query was ambiguous. Multiple possible variants found:

• chr3-15367319-G-C
• chr3-15367319-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 0.262 in 152,124 control chromosomes in the GnomAD database, including 5,647 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 0.26 (5647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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: 0.262 AC: 39890 AN: 152006 Hom.: 5646 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.262 AC: 39892 AN: 152124 Hom.: 5647 Cov.: 32 AF XY: 0.259 AC XY: 19235 AN XY: 74334

African (AFR) AF: 0.146 AC: 6070 AN: 41516

American (AMR) AF: 0.281 AC: 4301 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5174

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2721 AN: 10586

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21394 AN: 67956

Other (OTH) AF: 0.287 AC: 607 AN: 2116

Alfa AF: 0.277 Hom.: 745

Bravo AF: 0.262

Asia WGS AF: 0.284 AC: 984 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.4
DANN	Benign	0.59
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7629693; hg19: chr3-15408826;