rs1859943

Positions:

• chr12-125842022-A-G
• chr12-125842022-A-T

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 0.58 in 151,844 control chromosomes in the GnomAD database, including 25,760 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 0.58 (25760 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87980 AN: 151724 Hom.: 25729 Cov.: 30

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.580 AC: 88050 AN: 151844 Hom.: 25760 Cov.: 30 AF XY: 0.580 AC XY: 43014 AN XY: 74174

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.627

Alfa AF: 0.563 Hom.: 49259

Bravo AF: 0.597

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1859943; hg19: chr12-126326568;