15-101262360-T-C

Variant names:

• chr15-101262360-T-C
• rs12910524

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 0.738 in 151,998 control chromosomes in the GnomAD database, including 42,592 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 0.74 (42592 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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: 0.738 AC: 112059 AN: 151880 Hom.: 42541 Cov.: 30

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.738 AC: 112167 AN: 151998 Hom.: 42592 Cov.: 30 AF XY: 0.732 AC XY: 54408 AN XY: 74280

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.750

Alfa AF: 0.684 Hom.: 45598

Bravo AF: 0.757

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12910524; hg19: chr15-101802565;