chr12-12353249-GT-G

Variant names:

• chr12-12353249-GT-G
• rs11313889

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (31663 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.638 AC: 96952 AN: 151942 Hom.: 31655 Cov.: 0

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.638 AC: 97008 AN: 152060 Hom.: 31663 Cov.: 0 AF XY: 0.646 AC XY: 48015 AN XY: 74324

African (AFR) AF: 0.500 AC: 20717 AN: 41464

American (AMR) AF: 0.761 AC: 11637 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2572 AN: 3468

East Asian (EAS) AF: 0.846 AC: 4379 AN: 5178

South Asian (SAS) AF: 0.761 AC: 3673 AN: 4824

European-Finnish (FIN) AF: 0.653 AC: 6901 AN: 10574

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45098 AN: 67940

Other (OTH) AF: 0.677 AC: 1432 AN: 2114

Alfa AF: 0.648 Hom.: 3889

Bravo AF: 0.641

Asia WGS AF: 0.783 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11313889; hg19: chr12-12506183;