rs10519186

Positions:

• chr15-62921658-C-T

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 0.182 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.201

Alfa AF: 0.183 Hom.: 1517

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519186; hg19: chr15-63213857;