rs682359

Variant names:

• chr15-42134635-G-T
• rs682359

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 0.65 in 152,162 control chromosomes in the GnomAD database, including 33,609 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 0.65 (33609 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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: 0.650 AC: 98868 AN: 152044 Hom.: 33560 Cov.: 34

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.650 AC: 98965 AN: 152162 Hom.: 33609 Cov.: 34 AF XY: 0.646 AC XY: 48060 AN XY: 74386

African (AFR) AF: 0.848 AC: 35241 AN: 41558

American (AMR) AF: 0.502 AC: 7676 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2457 AN: 5156

South Asian (SAS) AF: 0.574 AC: 2768 AN: 4822

European-Finnish (FIN) AF: 0.636 AC: 6732 AN: 10588

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39868 AN: 67970

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.598 Hom.: 57932

Bravo AF: 0.649

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.63
DANN	Benign	0.57
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs682359; hg19: chr15-42426833;