rs371606

Variant names:

• chr15-66964426-T-G
• rs371606

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 0.583 in 151,974 control chromosomes in the GnomAD database, including 26,274 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 0.58 (26274 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.583 AC: 88461 AN: 151856 Hom.: 26245 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.583 AC: 88535 AN: 151974 Hom.: 26274 Cov.: 32 AF XY: 0.581 AC XY: 43142 AN XY: 74264

African (AFR) AF: 0.712 AC: 29510 AN: 41474

American (AMR) AF: 0.472 AC: 7203 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3470

East Asian (EAS) AF: 0.415 AC: 2135 AN: 5150

South Asian (SAS) AF: 0.577 AC: 2773 AN: 4806

European-Finnish (FIN) AF: 0.556 AC: 5856 AN: 10526

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37525 AN: 67960

Other (OTH) AF: 0.551 AC: 1162 AN: 2108

Alfa AF: 0.556 Hom.: 9360

Bravo AF: 0.577

Asia WGS AF: 0.466 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs371606; hg19: chr15-67256764;