12-69133998-C-T

Variant names:

• chr12-69133998-C-T
• rs12425617

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 0.377 in 151,882 control chromosomes in the GnomAD database, including 11,660 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 0.38 (11660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57222 AN: 151764 Hom.: 11663 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.377 AC: 57235 AN: 151882 Hom.: 11660 Cov.: 31 AF XY: 0.387 AC XY: 28691 AN XY: 74206

African (AFR) AF: 0.239 AC: 9906 AN: 41434

American (AMR) AF: 0.467 AC: 7122 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3466

East Asian (EAS) AF: 0.710 AC: 3663 AN: 5160

South Asian (SAS) AF: 0.525 AC: 2525 AN: 4812

European-Finnish (FIN) AF: 0.439 AC: 4630 AN: 10538

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26500 AN: 67914

Other (OTH) AF: 0.409 AC: 860 AN: 2102

Alfa AF: 0.393 Hom.: 20923

Bravo AF: 0.374

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.54
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12425617; hg19: chr12-69527778;