chr12-58126028-A-G

Variant names:

• chr12-58126028-A-G
• rs1848125

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 0.552 in 151,964 control chromosomes in the GnomAD database, including 24,644 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 (24644 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83786 AN: 151846 Hom.: 24604 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.552 AC: 83877 AN: 151964 Hom.: 24644 Cov.: 31 AF XY: 0.552 AC XY: 40987 AN XY: 74272

African (AFR) AF: 0.766 AC: 31785 AN: 41470

American (AMR) AF: 0.463 AC: 7072 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1808 AN: 5176

South Asian (SAS) AF: 0.512 AC: 2455 AN: 4798

European-Finnish (FIN) AF: 0.514 AC: 5427 AN: 10552

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32306 AN: 67918

Other (OTH) AF: 0.507 AC: 1068 AN: 2108

Alfa AF: 0.488 Hom.: 79477

Bravo AF: 0.554

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.55
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1848125; hg19: chr12-58519811;