chr11-129695521-C-T

Variant names:

• chr11-129695521-C-T
• rs1814344

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 0.655 in 152,198 control chromosomes in the GnomAD database, including 33,696 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 0.65 (33696 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.97
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 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: 0.655 AC: 99561 AN: 152080 Hom.: 33668 Cov.: 34

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.655 AC: 99648 AN: 152198 Hom.: 33696 Cov.: 34 AF XY: 0.659 AC XY: 49059 AN XY: 74410

African (AFR) AF: 0.483 AC: 20040 AN: 41510

American (AMR) AF: 0.616 AC: 9429 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3472

East Asian (EAS) AF: 0.741 AC: 3833 AN: 5174

South Asian (SAS) AF: 0.832 AC: 4014 AN: 4822

European-Finnish (FIN) AF: 0.768 AC: 8139 AN: 10604

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49296 AN: 67988

Other (OTH) AF: 0.668 AC: 1414 AN: 2116

Alfa AF: 0.678 Hom.: 10052

Bravo AF: 0.632

Asia WGS AF: 0.764 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.036
DANN	Benign	0.28
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs1814344; hg19: chr11-129565416;