11-128826702-C-T

Variant names:

• chr11-128826702-C-T
• rs588407

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 0.136 in 150,558 control chromosomes in the GnomAD database, including 1,414 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 0.14 (1414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 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 (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20392 AN: 150438 Hom.: 1410 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.136 AC: 20420 AN: 150558 Hom.: 1414 Cov.: 33 AF XY: 0.136 AC XY: 9998 AN XY: 73606

African (AFR) AF: 0.126 AC: 5077 AN: 40252

American (AMR) AF: 0.0898 AC: 1366 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3460

East Asian (EAS) AF: 0.0986 AC: 504 AN: 5114

South Asian (SAS) AF: 0.190 AC: 901 AN: 4752

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10568

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10090 AN: 67902

Other (OTH) AF: 0.124 AC: 260 AN: 2104

Alfa AF: 0.137 Hom.: 2671

Bravo AF: 0.126

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs588407; hg19: chr11-128696597;