12-128991394-A-G

Position:

• chr12-128991394-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;