rs10894119

Positions:

• chr11-129706331-C-T

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 0.141 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0703

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.128

Alfa AF: 0.162 Hom.: 660

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10894119; hg19: chr11-129576226;