rs12901373

chr15-50273643-C-Achr15-50273643-C-G

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 0.685 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.678

Alfa AF: 0.650 Hom.: 3872

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12901373; hg19: chr15-50565840;