rs12402879

Variant names:

• chr1-160581223-A-G
• rs12402879

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 0.508 in 151,790 control chromosomes in the GnomAD database, including 20,964 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 0.51 (20964 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 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: 0.508 AC: 77101 AN: 151672 Hom.: 20953 Cov.: 29

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.508 AC: 77148 AN: 151790 Hom.: 20964 Cov.: 29 AF XY: 0.513 AC XY: 38036 AN XY: 74154

African (AFR) AF: 0.314 AC: 13002 AN: 41404

American (AMR) AF: 0.467 AC: 7105 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1946 AN: 3462

East Asian (EAS) AF: 0.660 AC: 3398 AN: 5146

South Asian (SAS) AF: 0.545 AC: 2614 AN: 4792

European-Finnish (FIN) AF: 0.683 AC: 7189 AN: 10518

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40167 AN: 67928

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.553 Hom.: 8340

Bravo AF: 0.484

Asia WGS AF: 0.553 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs12402879; hg19: chr1-160551013;