chr11-116714271-C-T

Variant names:

• chr11-116714271-C-T
• rs4938303

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 0.621 in 151,864 control chromosomes in the GnomAD database, including 30,338 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 0.62 (30338 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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: 0.621 AC: 94305 AN: 151744 Hom.: 30341 Cov.: 30

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.621 AC: 94324 AN: 151864 Hom.: 30338 Cov.: 30 AF XY: 0.612 AC XY: 45431 AN XY: 74212

African (AFR) AF: 0.479 AC: 19809 AN: 41364

American (AMR) AF: 0.578 AC: 8823 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2671 AN: 5134

South Asian (SAS) AF: 0.421 AC: 2029 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7052 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49276 AN: 67970

Other (OTH) AF: 0.636 AC: 1339 AN: 2106

Alfa AF: 0.687 Hom.: 115214

Bravo AF: 0.613

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs4938303; hg19: chr11-116584987; COSMIC: COSV107159454;