rs17113682

Variant names:

• chr10-101085484-G-A
• rs17113682

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0585 AC: 2428 AN: 41472

American (AMR) AF: 0.229 AC: 3503 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5152

South Asian (SAS) AF: 0.260 AC: 1247 AN: 4794

European-Finnish (FIN) AF: 0.252 AC: 2663 AN: 10588

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14450 AN: 67932

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.196 Hom.: 6296

Bravo AF: 0.170

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.1
DANN	Benign	0.51
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs17113682; hg19: chr10-102845241;