12-132169401-T-A

Variant names:

• chr12-132169401-T-A
• rs7133868

Variant summary

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

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 0.11 (850 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.112 AC: 5578 AN: 49598 Hom.: 849 Cov.: 0

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0781

Gnomad ASJ AF: 0.0419

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.112 AC: 5580 AN: 49604 Hom.: 850 Cov.: 0 AF XY: 0.106 AC XY: 2590 AN XY: 24482

African (AFR) AF: 0.156 AC: 993 AN: 6348

American (AMR) AF: 0.0778 AC: 466 AN: 5986

Ashkenazi Jewish (ASJ) AF: 0.0419 AC: 57 AN: 1360

East Asian (EAS) AF: 0.0374 AC: 124 AN: 3316

South Asian (SAS) AF: 0.0858 AC: 136 AN: 1586

European-Finnish (FIN) AF: 0.0932 AC: 400 AN: 4292

Middle Eastern (MID) AF: 0.117 AC: 15 AN: 128

European-Non Finnish (NFE) AF: 0.128 AC: 3285 AN: 25684

Other (OTH) AF: 0.112 AC: 81 AN: 724

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.5

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: rs7133868; hg19: chr12-132653946;