chr11-129695656-C-T

Variant names:

• chr11-129695656-C-T
• rs4937447

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.522

Alfa AF: 0.526 Hom.: 4186

Bravo AF: 0.464

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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