chr11-129695656-C-T

Variant names:

• chr11-129695656-C-T
• rs4937447

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 0.481 in 152,118 control chromosomes in the GnomAD database, including 18,564 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 0.48 (18564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.683 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: 0.481 AC: 73123 AN: 152000 Hom.: 18553 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.481 AC: 73176 AN: 152118 Hom.: 18564 Cov.: 33 AF XY: 0.480 AC XY: 35669 AN XY: 74346

African (AFR) AF: 0.339 AC: 14068 AN: 41536

American (AMR) AF: 0.423 AC: 6465 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2081 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2552 AN: 5128

South Asian (SAS) AF: 0.703 AC: 3395 AN: 4828

European-Finnish (FIN) AF: 0.481 AC: 5089 AN: 10584

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.557 AC: 37862 AN: 67966

Other (OTH) AF: 0.522 AC: 1102 AN: 2112

Alfa AF: 0.468 Hom.: 7633

Bravo AF: 0.464

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.3
DANN	Benign	0.83
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4937447; hg19: chr11-129565551; COSMIC: COSV68560703;