11-129697815-A-G

Variant names:

• chr11-129697815-A-G
• rs10894116

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 0.784 in 152,028 control chromosomes in the GnomAD database, including 50,450 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 0.78 (50450 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119199 AN: 151910 Hom.: 50447 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.784 AC: 119245 AN: 152028 Hom.: 50450 Cov.: 32 AF XY: 0.789 AC XY: 58660 AN XY: 74302

African (AFR) AF: 0.431 AC: 17825 AN: 41356

American (AMR) AF: 0.861 AC: 13166 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3163 AN: 3470

East Asian (EAS) AF: 0.830 AC: 4265 AN: 5140

South Asian (SAS) AF: 0.962 AC: 4641 AN: 4824

European-Finnish (FIN) AF: 0.943 AC: 10001 AN: 10604

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63347 AN: 68016

Other (OTH) AF: 0.824 AC: 1743 AN: 2116

Alfa AF: 0.881 Hom.: 177425

Bravo AF: 0.758

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.8
DANN	Benign	0.83
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10894116; hg19: chr11-129567710;