12-128790482-G-A

Variant names:

• chr12-128790482-G-A
• rs6486730

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 0.551 in 151,972 control chromosomes in the GnomAD database, including 23,377 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 0.55 (23377 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.551 AC: 83709 AN: 151854 Hom.: 23364 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.551 AC: 83767 AN: 151972 Hom.: 23377 Cov.: 31 AF XY: 0.550 AC XY: 40857 AN XY: 74272

African (AFR) AF: 0.503 AC: 20871 AN: 41472

American (AMR) AF: 0.459 AC: 7008 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3470

East Asian (EAS) AF: 0.452 AC: 2324 AN: 5146

South Asian (SAS) AF: 0.578 AC: 2785 AN: 4820

European-Finnish (FIN) AF: 0.624 AC: 6580 AN: 10540

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40229 AN: 67952

Other (OTH) AF: 0.523 AC: 1105 AN: 2114

Alfa AF: 0.521 Hom.: 4954

Bravo AF: 0.535

Asia WGS AF: 0.473 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.75
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs6486730; hg19: chr12-129275027;