rs682359

Positions:

• chr15-42134635-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 0.65 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.612

Alfa AF: 0.594 Hom.: 38294

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs682359; hg19: chr15-42426833;