11-111310395-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.454

Alfa AF: 0.492 Hom.: 27615

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

Splicing

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

Publications

LitVar

Other links and lift over

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