rs7629693

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;