12-131855412-T-C

Variant names:

• chr12-131855412-T-C
• rs4964933

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 0.873 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.711 AC: 29473 AN: 41480

American (AMR) AF: 0.887 AC: 13568 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3317 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3426 AN: 5138

South Asian (SAS) AF: 0.869 AC: 4181 AN: 4814

European-Finnish (FIN) AF: 0.972 AC: 10295 AN: 10596

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.965 AC: 65650 AN: 68028

Other (OTH) AF: 0.870 AC: 1839 AN: 2114

Alfa AF: 0.935 Hom.: 108814

Bravo AF: 0.856

Asia WGS AF: 0.774 AC: 2689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.6
DANN	Benign	0.91
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4964933; hg19: chr12-132339957;