rs12793759

chr11-69207088-G-A

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 0.115 in 151,992 control chromosomes in the GnomAD database, including 1,172 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 0.12 (1172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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: 0.115 AC: 17492 AN: 151874 Hom.: 1172 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0147

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.115 AC: 17485 AN: 151992 Hom.: 1172 Cov.: 32 AF XY: 0.112 AC XY: 8296 AN XY: 74282

Gnomad4 AFR AF: 0.0635

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.149

Alfa AF: 0.139 Hom.: 477

Bravo AF: 0.117

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	3.9
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12793759; hg19: chr11-68974555;