rs12289502

Variant names:

• chr11-80688369-A-C
• rs12289502

Your query was ambiguous. Multiple possible variants found:

• chr11-80688369-A-C
• chr11-80688369-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.534 in 152,040 control chromosomes in the GnomAD database, including 25,150 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 0.53 (25150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81148 AN: 151922 Hom.: 25134 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.534 AC: 81180 AN: 152040 Hom.: 25150 Cov.: 32 AF XY: 0.538 AC XY: 40005 AN XY: 74294

African (AFR) AF: 0.208 AC: 8636 AN: 41520

American (AMR) AF: 0.675 AC: 10299 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3466

East Asian (EAS) AF: 0.334 AC: 1720 AN: 5150

South Asian (SAS) AF: 0.728 AC: 3514 AN: 4824

European-Finnish (FIN) AF: 0.656 AC: 6917 AN: 10546

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46047 AN: 67962

Other (OTH) AF: 0.537 AC: 1136 AN: 2114

Alfa AF: 0.528 Hom.: 3169

Bravo AF: 0.517

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.66
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12289502; hg19: chr11-80399413;