rs1848125

Variant names:

• chr12-58126028-A-G
• rs1848125

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 0.552 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.552 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

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.507

Alfa AF: 0.473 Hom.: 34754

Bravo AF: 0.554

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1848125; hg19: chr12-58519811;