rs17120035

chr11-116793135-C-T

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 0.0663 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0491

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.0759

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0720 Hom.: 338

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17120035; hg19: chr11-116663851;