12-131855412-T-C

Position:

• chr12-131855412-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 0.873 in 152,146 control chromosomes in the GnomAD database, including 58,944 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 0.87 (58944 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.131855412T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132723 AN: 152028 Hom.: 58918 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.873 AC: 132800 AN: 152146 Hom.: 58944 Cov.: 32 AF XY: 0.870 AC XY: 64680 AN XY: 74350

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.870

Alfa AF: 0.945 Hom.: 86906

Bravo AF: 0.856

Asia WGS AF: 0.774 AC: 2689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.6
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4964933; hg19: chr12-132339957;