chr15-101262360-T-C

Variant names:

• chr15-101262360-T-C
• rs12910524

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 0.738 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.925 AC: 38398 AN: 41502

American (AMR) AF: 0.719 AC: 10979 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2551 AN: 3468

East Asian (EAS) AF: 0.647 AC: 3338 AN: 5160

South Asian (SAS) AF: 0.603 AC: 2894 AN: 4796

European-Finnish (FIN) AF: 0.604 AC: 6379 AN: 10560

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45469 AN: 67936

Other (OTH) AF: 0.750 AC: 1578 AN: 2104

Alfa AF: 0.698 Hom.: 110599

Bravo AF: 0.757

Asia WGS AF: 0.657 AC: 2284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.63
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs12910524; hg19: chr15-101802565;