rs10894119

Variant names:

• chr11-129706331-C-T
• rs10894119

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 0.141 in 152,046 control chromosomes in the GnomAD database, including 1,804 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 0.14 (1804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.179 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: 0.142 AC: 21502 AN: 151928 Hom.: 1805 Cov.: 31

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.141 AC: 21503 AN: 152046 Hom.: 1804 Cov.: 31 AF XY: 0.142 AC XY: 10575 AN XY: 74298

African (AFR) AF: 0.0703 AC: 2916 AN: 41492

American (AMR) AF: 0.0868 AC: 1326 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3468

East Asian (EAS) AF: 0.111 AC: 575 AN: 5164

South Asian (SAS) AF: 0.0839 AC: 403 AN: 4804

European-Finnish (FIN) AF: 0.258 AC: 2721 AN: 10556

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12347 AN: 67970

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.156 Hom.: 961

Bravo AF: 0.127

Asia WGS AF: 0.0820 AC: 285 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	2.9
DANN	Benign	0.63
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs10894119; hg19: chr11-129576226;