rs10894294

Variant names:

• chr11-130960853-C-A
• rs10894294

Your query was ambiguous. Multiple possible variants found:

• chr11-130960853-C-A
• chr11-130960853-C-G
• chr11-130960853-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 0.569 in 151,850 control chromosomes in the GnomAD database, including 25,492 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 0.57 (25492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 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: 0.569 AC: 86262 AN: 151732 Hom.: 25457 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.569 AC: 86354 AN: 151850 Hom.: 25492 Cov.: 32 AF XY: 0.565 AC XY: 41906 AN XY: 74210

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.542

Alfa AF: 0.533 Hom.: 6634

Bravo AF: 0.578

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10894294; hg19: chr11-130830748;