12-42608626-G-A

Variant names:

• chr12-42608626-G-A
• rs6582406

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 0.418 in 151,906 control chromosomes in the GnomAD database, including 13,423 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 0.42 (13423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.418 AC: 63397 AN: 151788 Hom.: 13417 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.418 AC: 63425 AN: 151906 Hom.: 13423 Cov.: 32 AF XY: 0.417 AC XY: 30956 AN XY: 74244

African (AFR) AF: 0.360 AC: 14890 AN: 41408

American (AMR) AF: 0.439 AC: 6712 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2229 AN: 5156

South Asian (SAS) AF: 0.392 AC: 1881 AN: 4804

European-Finnish (FIN) AF: 0.426 AC: 4483 AN: 10530

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29977 AN: 67954

Other (OTH) AF: 0.443 AC: 933 AN: 2108

Alfa AF: 0.343 Hom.: 1373

Bravo AF: 0.416

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.6
DANN	Benign	0.79
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs6582406; hg19: chr12-43002428;