15-50273643-C-A

Variant names:

• chr15-50273643-C-A
• rs12901373

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 0.685 in 152,026 control chromosomes in the GnomAD database, including 36,532 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 0.68 (36532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.685 AC: 104012 AN: 151910 Hom.: 36488 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.685 AC: 104113 AN: 152026 Hom.: 36532 Cov.: 32 AF XY: 0.676 AC XY: 50225 AN XY: 74332

African (AFR) AF: 0.819 AC: 33998 AN: 41490

American (AMR) AF: 0.707 AC: 10814 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2602 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1829 AN: 5174

South Asian (SAS) AF: 0.553 AC: 2667 AN: 4822

European-Finnish (FIN) AF: 0.548 AC: 5770 AN: 10528

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.650 AC: 44180 AN: 67946

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

Alfa AF: 0.658 Hom.: 4142

Bravo AF: 0.707

Asia WGS AF: 0.458 AC: 1592 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.64
DANN	Benign	0.44
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12901373; hg19: chr15-50565840;