15-101262360-T-C

Position:

• chr15-101262360-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;