12-50486433-T-C

Variant names:

• chr12-50486433-T-C
• rs7136702

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.593

Alfa AF: 0.643 Hom.: 51782

Bravo AF: 0.562

Asia WGS AF: 0.510 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7136702; hg19: chr12-50880216;