chr12-50486433-T-C

Variant names:

• chr12-50486433-T-C
• rs7136702

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 0.576 in 151,950 control chromosomes in the GnomAD database, including 26,378 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 0.58 (26378 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 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: 0.576 AC: 87438 AN: 151832 Hom.: 26350 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.576 AC: 87518 AN: 151950 Hom.: 26378 Cov.: 31 AF XY: 0.580 AC XY: 43082 AN XY: 74290

African (AFR) AF: 0.403 AC: 16683 AN: 41390

American (AMR) AF: 0.613 AC: 9360 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2271 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2777 AN: 5156

South Asian (SAS) AF: 0.471 AC: 2266 AN: 4814

European-Finnish (FIN) AF: 0.721 AC: 7626 AN: 10578

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44400 AN: 67970

Other (OTH) AF: 0.593 AC: 1252 AN: 2110

Alfa AF: 0.634 Hom.: 103121

Bravo AF: 0.562

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.60
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7136702; hg19: chr12-50880216;