rs10515083

Variant names:

• chr17-54886696-T-A
• rs10515083

Your query was ambiguous. Multiple possible variants found:

• chr17-54886696-T-A
• chr17-54886696-T-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.458 in 151,936 control chromosomes in the GnomAD database, including 16,901 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 0.46 (16901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 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: 0.458 AC: 69531 AN: 151820 Hom.: 16899 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.458 AC: 69561 AN: 151936 Hom.: 16901 Cov.: 32 AF XY: 0.454 AC XY: 33699 AN XY: 74262

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.471

Alfa AF: 0.510 Hom.: 2584

Bravo AF: 0.445

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	17
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515083; hg19: chr17-52964057;