rs17120035

Variant names:

• chr11-116793135-C-T
• rs17120035

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 0.0663 in 152,282 control chromosomes in the GnomAD database, including 497 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 0.066 (497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 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: 0.0664 AC: 10105 AN: 152164 Hom.: 498 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0491

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0663 AC: 10093 AN: 152282 Hom.: 497 Cov.: 32 AF XY: 0.0698 AC XY: 5196 AN XY: 74446

African (AFR) AF: 0.0353 AC: 1466 AN: 41574

American (AMR) AF: 0.0438 AC: 670 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0491 AC: 170 AN: 3464

East Asian (EAS) AF: 0.0717 AC: 372 AN: 5190

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4826

European-Finnish (FIN) AF: 0.0997 AC: 1056 AN: 10594

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0759 AC: 5161 AN: 68014

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0698 Hom.: 941

Bravo AF: 0.0579

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.80
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs17120035; hg19: chr11-116663851;