chr12-112936943-C-T

Position:

• chr12-112936943-C-T

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 0.593 in 152,050 control chromosomes in the GnomAD database, including 27,828 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 0.59 (27828 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.112936943C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257452	ENST00000552784.1	n.354-28265G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.592 AC: 90005 AN: 151932 Hom.: 27798 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.593 AC: 90098 AN: 152050 Hom.: 27828 Cov.: 32 AF XY: 0.601 AC XY: 44674 AN XY: 74314

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.595

Alfa AF: 0.628 Hom.: 41703

Bravo AF: 0.582

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
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: rs10774679; hg19: chr12-113374748;