11-111310395-C-T

Variant names:

• chr11-111310395-C-T
• rs7947952

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.395 in 151,924 control chromosomes in the GnomAD database, including 13,807 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 0.40 (13807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.396 AC: 60065 AN: 151806 Hom.: 13802 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.395 AC: 60081 AN: 151924 Hom.: 13807 Cov.: 32 AF XY: 0.392 AC XY: 29091 AN XY: 74236

African (AFR) AF: 0.147 AC: 6087 AN: 41540

American (AMR) AF: 0.449 AC: 6862 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3466

East Asian (EAS) AF: 0.429 AC: 2216 AN: 5166

South Asian (SAS) AF: 0.408 AC: 1958 AN: 4804

European-Finnish (FIN) AF: 0.431 AC: 4551 AN: 10560

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35245 AN: 67814

Other (OTH) AF: 0.454 AC: 961 AN: 2116

Alfa AF: 0.475 Hom.: 67055

Bravo AF: 0.392

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	8.9
DANN	Benign	0.72
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7947952; hg19: chr11-111181120; COSMIC: COSV67695315;