12-50056193-T-C

Position:

• chr12-50056193-T-C

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 0.629 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.647

Alfa AF: 0.642 Hom.: 39754

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs590460; hg19: chr12-50449976;