12-131855412-T-C

Variant names:

• chr12-131855412-T-C
• rs4964933

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;