rs10519010

chr15-60259727-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;