15-85919621-T-C

Variant names:

• chr15-85919621-T-C
• rs4262906

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 0.501 in 152,102 control chromosomes in the GnomAD database, including 21,059 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 0.50 (21059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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: 0.500 AC: 76030 AN: 151984 Hom.: 21018 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.501 AC: 76130 AN: 152102 Hom.: 21059 Cov.: 32 AF XY: 0.494 AC XY: 36702 AN XY: 74346

African (AFR) AF: 0.752 AC: 31205 AN: 41476

American (AMR) AF: 0.443 AC: 6771 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2556 AN: 5160

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4814

European-Finnish (FIN) AF: 0.283 AC: 2999 AN: 10592

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27263 AN: 67976

Other (OTH) AF: 0.481 AC: 1014 AN: 2110

Alfa AF: 0.434 Hom.: 62651

Bravo AF: 0.521

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.35
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4262906; hg19: chr15-86462852;