chr12-129906479-C-A

Variant names:

• chr12-129906479-C-A
• rs478347

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 0.504 in 151,986 control chromosomes in the GnomAD database, including 19,451 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 0.50 (19451 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.504 AC: 76516 AN: 151868 Hom.: 19423 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.504 AC: 76571 AN: 151986 Hom.: 19451 Cov.: 33 AF XY: 0.499 AC XY: 37043 AN XY: 74288

African (AFR) AF: 0.484 AC: 20088 AN: 41464

American (AMR) AF: 0.508 AC: 7761 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3207 AN: 5144

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4816

European-Finnish (FIN) AF: 0.442 AC: 4664 AN: 10560

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36055 AN: 67942

Other (OTH) AF: 0.502 AC: 1060 AN: 2110

Alfa AF: 0.514 Hom.: 33778

Bravo AF: 0.506

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.49
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs478347; hg19: chr12-130391024;