rs1859943

Variant names:

• chr12-125842022-A-G
• rs1859943

Your query was ambiguous. Multiple possible variants found:

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

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 0.58 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.610 AC: 25233 AN: 41368

American (AMR) AF: 0.703 AC: 10731 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2079 AN: 3466

East Asian (EAS) AF: 0.585 AC: 3001 AN: 5128

South Asian (SAS) AF: 0.579 AC: 2783 AN: 4804

European-Finnish (FIN) AF: 0.485 AC: 5119 AN: 10546

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.547 AC: 37178 AN: 67950

Other (OTH) AF: 0.627 AC: 1323 AN: 2110

Alfa AF: 0.566 Hom.: 77729

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1859943; hg19: chr12-126326568;