11-57029977-A-G

Variant names:

• chr11-57029977-A-G
• rs501828

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 0.464 in 152,058 control chromosomes in the GnomAD database, including 16,885 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 0.46 (16885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70547 AN: 151940 Hom.: 16866 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.464 AC: 70600 AN: 152058 Hom.: 16885 Cov.: 32 AF XY: 0.464 AC XY: 34487 AN XY: 74348

African (AFR) AF: 0.564 AC: 23384 AN: 41440

American (AMR) AF: 0.451 AC: 6897 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3055 AN: 5176

South Asian (SAS) AF: 0.415 AC: 2003 AN: 4826

European-Finnish (FIN) AF: 0.401 AC: 4240 AN: 10586

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28536 AN: 67964

Other (OTH) AF: 0.442 AC: 933 AN: 2112

Alfa AF: 0.357 Hom.: 1818

Bravo AF: 0.475

Asia WGS AF: 0.451 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs501828; hg19: chr11-56797452;