rs10515101

Variant names:

• chr17-55437171-A-G
• rs10515101

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 0.164 in 152,118 control chromosomes in the GnomAD database, including 2,078 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 0.16 (2078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 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: 0.164 AC: 24875 AN: 152000 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.164 AC: 24888 AN: 152118 Hom.: 2078 Cov.: 32 AF XY: 0.165 AC XY: 12240 AN XY: 74358

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.161

Alfa AF: 0.185 Hom.: 2720

Bravo AF: 0.162

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.017
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515101; hg19: chr17-53514532;