chr11-129369889-T-C

Variant names:

• chr11-129369889-T-C
• rs10894032

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 0.501 in 151,926 control chromosomes in the GnomAD database, including 19,690 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 0.50 (19690 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76084 AN: 151806 Hom.: 19650 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.501 AC: 76177 AN: 151926 Hom.: 19690 Cov.: 31 AF XY: 0.510 AC XY: 37852 AN XY: 74278

African (AFR) AF: 0.407 AC: 16852 AN: 41430

American (AMR) AF: 0.592 AC: 9032 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3464

East Asian (EAS) AF: 0.680 AC: 3504 AN: 5156

South Asian (SAS) AF: 0.698 AC: 3354 AN: 4804

European-Finnish (FIN) AF: 0.532 AC: 5624 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34204 AN: 67930

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.514 Hom.: 26407

Bravo AF: 0.499

Asia WGS AF: 0.703 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.68
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10894032; hg19: chr11-129239784;