rs11017516

Variant names:

• chr10-130850180-T-C
• rs11017516

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 0.0786 in 152,086 control chromosomes in the GnomAD database, including 502 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 0.079 (502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 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: 0.0786 AC: 11937 AN: 151966 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0786 AC: 11954 AN: 152086 Hom.: 502 Cov.: 32 AF XY: 0.0777 AC XY: 5778 AN XY: 74336

African (AFR) AF: 0.0775 AC: 3217 AN: 41492

American (AMR) AF: 0.0545 AC: 831 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5174

South Asian (SAS) AF: 0.0563 AC: 271 AN: 4810

European-Finnish (FIN) AF: 0.105 AC: 1115 AN: 10570

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0897 AC: 6099 AN: 67992

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0828 Hom.: 428

Bravo AF: 0.0741

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11017516; hg19: chr10-132648443; COSMIC: COSV51508385;