rs12794435

Variant names:

• chr11-25186158-G-A
• rs12794435

Your query was ambiguous. Multiple possible variants found:

• chr11-25186158-G-A
• chr11-25186158-G-C

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 0.0752 in 151,840 control chromosomes in the GnomAD database, including 556 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 0.075 (556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0753 AC: 11420 AN: 151722 Hom.: 556 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0583

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.000775

Gnomad SAS AF: 0.0833

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0752 AC: 11417 AN: 151840 Hom.: 556 Cov.: 32 AF XY: 0.0740 AC XY: 5491 AN XY: 74218

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.000777

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.104 Hom.: 1130

Bravo AF: 0.0701

Asia WGS AF: 0.0370 AC: 129 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12794435; hg19: chr11-25207704; COSMIC: COSV54092863;