chr12-126590601-A-G

Variant names:

• chr12-126590601-A-G
• rs2058290

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 0.871 in 152,214 control chromosomes in the GnomAD database, including 57,834 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 0.87 (57834 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.871 AC: 132460 AN: 152096 Hom.: 57774 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.871 AC: 132579 AN: 152214 Hom.: 57834 Cov.: 33 AF XY: 0.872 AC XY: 64911 AN XY: 74406

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.887

Alfa AF: 0.872 Hom.: 78831

Bravo AF: 0.875

Asia WGS AF: 0.964 AC: 3353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058290; hg19: chr12-127075147;