11-126281347-T-C

Variant names:

• chr11-126281347-T-C
• rs655540

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 0.175 in 151,948 control chromosomes in the GnomAD database, including 2,737 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 0.17 (2737 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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: 0.175 AC: 26563 AN: 151844 Hom.: 2735 Cov.: 31

Gnomad AFR AF: 0.0877

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.175 AC: 26570 AN: 151948 Hom.: 2737 Cov.: 31 AF XY: 0.168 AC XY: 12502 AN XY: 74226

African (AFR) AF: 0.0877 AC: 3635 AN: 41450

American (AMR) AF: 0.133 AC: 2030 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3472

East Asian (EAS) AF: 0.0337 AC: 174 AN: 5160

South Asian (SAS) AF: 0.152 AC: 729 AN: 4810

European-Finnish (FIN) AF: 0.192 AC: 2018 AN: 10510

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16748 AN: 67964

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.136 Hom.: 311

Bravo AF: 0.165

Asia WGS AF: 0.0920 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs655540; hg19: chr11-126151242;