rs10519010

Variant names:

• chr15-60259727-C-A
• rs10519010

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 0.183 in 152,222 control chromosomes in the GnomAD database, including 2,846 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 (2846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 27759 AN: 152104 Hom.: 2835 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.183 AC: 27801 AN: 152222 Hom.: 2846 Cov.: 32 AF XY: 0.178 AC XY: 13215 AN XY: 74430

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.165

Alfa AF: 0.162 Hom.: 4241

Bravo AF: 0.184

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519010; hg19: chr15-60551926;