rs12792526

chr11-130659324-A-Gchr11-130659324-A-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 151,836 control chromosomes in the GnomAD database, including 2,109 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 (2109 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21388 AN: 151718 Hom.: 2114 Cov.: 31

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.141 AC: 21376 AN: 151836 Hom.: 2109 Cov.: 31 AF XY: 0.148 AC XY: 10954 AN XY: 74200

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.155

Alfa AF: 0.151 Hom.: 1650

Bravo AF: 0.146

Asia WGS AF: 0.261 AC: 904 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12792526; hg19: chr11-130529219;