15-62090956-T-C

Variant names:

• chr15-62090956-T-C
• rs4502156

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 0.545 in 152,062 control chromosomes in the GnomAD database, including 23,974 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 0.54 (23974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 85 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82738 AN: 151944 Hom.: 23918 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.545 AC: 82860 AN: 152062 Hom.: 23974 Cov.: 32 AF XY: 0.549 AC XY: 40795 AN XY: 74328

African (AFR) AF: 0.744 AC: 30839 AN: 41462

American (AMR) AF: 0.581 AC: 8871 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2542 AN: 5174

South Asian (SAS) AF: 0.475 AC: 2292 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6021 AN: 10578

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29435 AN: 67966

Other (OTH) AF: 0.521 AC: 1097 AN: 2106

Alfa AF: 0.463 Hom.: 66349

Bravo AF: 0.555

Asia WGS AF: 0.521 AC: 1810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.36
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4502156; hg19: chr15-62383155;