rs17113682

chr10-101085484-G-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 0.176 in 151,996 control chromosomes in the GnomAD database, including 2,834 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 (2834 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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: 0.176 AC: 26732 AN: 151878 Hom.: 2823 Cov.: 31

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.176 AC: 26761 AN: 151996 Hom.: 2834 Cov.: 31 AF XY: 0.182 AC XY: 13507 AN XY: 74304

Gnomad4 AFR AF: 0.0585

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.182

Alfa AF: 0.208 Hom.: 4841

Bravo AF: 0.170

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17113682; hg19: chr10-102845241;