rs2190679

Variant names:

• chr12-125835403-A-G
• rs2190679

Your query was ambiguous. Multiple possible variants found:

• chr12-125835403-A-G
• chr12-125835403-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 0.703 in 151,658 control chromosomes in the GnomAD database, including 39,029 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 0.70 (39029 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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: 0.703 AC: 106589 AN: 151566 Hom.: 38979 Cov.: 30

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.703 AC: 106678 AN: 151658 Hom.: 39029 Cov.: 30 AF XY: 0.704 AC XY: 52145 AN XY: 74074

African (AFR) AF: 0.917 AC: 37944 AN: 41376

American (AMR) AF: 0.758 AC: 11562 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2295 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3055 AN: 5134

South Asian (SAS) AF: 0.661 AC: 3162 AN: 4784

European-Finnish (FIN) AF: 0.592 AC: 6165 AN: 10416

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40297 AN: 67918

Other (OTH) AF: 0.718 AC: 1515 AN: 2110

Alfa AF: 0.604 Hom.: 12701

Bravo AF: 0.725

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2190679; hg19: chr12-126319949;