12-94133780-T-G

Variant names:

• chr12-94133780-T-G
• rs12099972

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 0.103 in 142,180 control chromosomes in the GnomAD database, including 781 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 0.10 (781 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.201 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: 0.103 AC: 14648 AN: 142064 Hom.: 777 Cov.: 29

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.103 AC: 14656 AN: 142180 Hom.: 781 Cov.: 29 AF XY: 0.106 AC XY: 7320 AN XY: 68854

African (AFR) AF: 0.130 AC: 4808 AN: 36950

American (AMR) AF: 0.110 AC: 1496 AN: 13614

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 146 AN: 3396

East Asian (EAS) AF: 0.211 AC: 1073 AN: 5078

South Asian (SAS) AF: 0.115 AC: 514 AN: 4454

European-Finnish (FIN) AF: 0.112 AC: 1076 AN: 9644

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0791 AC: 5213 AN: 65916

Other (OTH) AF: 0.106 AC: 205 AN: 1940

Alfa AF: 0.0800 Hom.: 876

Bravo AF: 0.102

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.77
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs12099972; hg19: chr12-94527556;