11-57394409-T-A

Position:

• chr11-57394409-T-A

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 0.719 in 152,084 control chromosomes in the GnomAD database, including 39,577 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 0.72 (39577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.719 AC: 109210 AN: 151966 Hom.: 39563 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.719 AC: 109276 AN: 152084 Hom.: 39577 Cov.: 32 AF XY: 0.723 AC XY: 53766 AN XY: 74356

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.726

Alfa AF: 0.654 Hom.: 1950

Bravo AF: 0.720

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs526572; hg19: chr11-57161882;