12-128991394-A-G

Variant names:

• chr12-128991394-A-G
• rs643473

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 0.722 in 151,950 control chromosomes in the GnomAD database, including 40,509 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 0.72 (40509 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.722 AC: 109624 AN: 151832 Hom.: 40466 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.722 AC: 109726 AN: 151950 Hom.: 40509 Cov.: 30 AF XY: 0.728 AC XY: 54093 AN XY: 74268

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.702

Alfa AF: 0.650 Hom.: 26891

Bravo AF: 0.732

Asia WGS AF: 0.817 AC: 2842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
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: rs643473; hg19: chr12-129475939;