chr12-50056193-T-C

Variant names:

• chr12-50056193-T-C
• rs590460

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 0.629 in 151,808 control chromosomes in the GnomAD database, including 30,520 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 0.63 (30520 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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: 0.629 AC: 95395 AN: 151690 Hom.: 30499 Cov.: 30

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.629 AC: 95464 AN: 151808 Hom.: 30520 Cov.: 30 AF XY: 0.635 AC XY: 47130 AN XY: 74196

African (AFR) AF: 0.527 AC: 21786 AN: 41344

American (AMR) AF: 0.700 AC: 10684 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2747 AN: 3464

East Asian (EAS) AF: 0.846 AC: 4355 AN: 5150

South Asian (SAS) AF: 0.589 AC: 2834 AN: 4814

European-Finnish (FIN) AF: 0.714 AC: 7543 AN: 10558

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43301 AN: 67910

Other (OTH) AF: 0.647 AC: 1357 AN: 2096

Alfa AF: 0.639 Hom.: 50233

Bravo AF: 0.626

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.3
DANN	Benign	0.33
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs590460; hg19: chr12-50449976;