rs10515083

Positions:

• 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/exons	MANE	UniProt

Ensembl

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