chr11-57592329-T-A

Variant names:

• chr11-57592329-T-A
• rs2244169

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 0.543 in 151,362 control chromosomes in the GnomAD database, including 22,833 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 0.54 (22833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82137 AN: 151242 Hom.: 22811 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.543 AC: 82209 AN: 151362 Hom.: 22833 Cov.: 31 AF XY: 0.549 AC XY: 40618 AN XY: 73934

African (AFR) AF: 0.577 AC: 23818 AN: 41262

American (AMR) AF: 0.591 AC: 8980 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2160 AN: 3466

East Asian (EAS) AF: 0.857 AC: 4402 AN: 5136

South Asian (SAS) AF: 0.605 AC: 2901 AN: 4794

European-Finnish (FIN) AF: 0.499 AC: 5223 AN: 10458

Middle Eastern (MID) AF: 0.653 AC: 188 AN: 288

European-Non Finnish (NFE) AF: 0.483 AC: 32704 AN: 67758

Other (OTH) AF: 0.546 AC: 1151 AN: 2108

Alfa AF: 0.528 Hom.: 2686

Bravo AF: 0.552

Asia WGS AF: 0.717 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2244169; hg19: chr11-57359802;