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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.262 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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.287

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7629693; hg19: chr3-15408826;