rs478347

chr12-129906479-C-A

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 0.504 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.502

Alfa AF: 0.516 Hom.: 26793

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs478347; hg19: chr12-130391024;