15-62921658-C-T

Variant names:

• chr15-62921658-C-T
• rs10519186

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 0.182 in 152,216 control chromosomes in the GnomAD database, including 3,015 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 0.18 (3015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.182 AC: 27716 AN: 152098 Hom.: 3012 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.182 AC: 27734 AN: 152216 Hom.: 3015 Cov.: 33 AF XY: 0.185 AC XY: 13766 AN XY: 74426

African (AFR) AF: 0.112 AC: 4651 AN: 41548

American (AMR) AF: 0.259 AC: 3964 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2604 AN: 5176

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4812

European-Finnish (FIN) AF: 0.143 AC: 1520 AN: 10596

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12189 AN: 68002

Other (OTH) AF: 0.201 AC: 425 AN: 2114

Alfa AF: 0.188 Hom.: 2695

Bravo AF: 0.190

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10519186; hg19: chr15-63213857;