rs10491113

Variant names:

• chr17-34677114-C-T
• rs10491113

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 0.165 in 152,130 control chromosomes in the GnomAD database, including 2,396 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 0.17 (2396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25118 AN: 152012 Hom.: 2393 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.165 AC: 25145 AN: 152130 Hom.: 2396 Cov.: 32 AF XY: 0.169 AC XY: 12545 AN XY: 74352

African (AFR) AF: 0.0895 AC: 3716 AN: 41532

American (AMR) AF: 0.268 AC: 4089 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 459 AN: 3464

East Asian (EAS) AF: 0.283 AC: 1459 AN: 5158

South Asian (SAS) AF: 0.155 AC: 746 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2476 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11724 AN: 67978

Other (OTH) AF: 0.166 AC: 350 AN: 2108

Alfa AF: 0.178 Hom.: 2053

Bravo AF: 0.169

Asia WGS AF: 0.205 AC: 712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs10491113; hg19: chr17-33004133;