rs1558789

Variant names:

• chr12-15015857-C-A
• rs1558789

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 0.429 in 151,788 control chromosomes in the GnomAD database, including 14,902 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 0.43 (14902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65112 AN: 151670 Hom.: 14907 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.429 AC: 65103 AN: 151788 Hom.: 14902 Cov.: 32 AF XY: 0.428 AC XY: 31711 AN XY: 74160

African (AFR) AF: 0.276 AC: 11414 AN: 41430

American (AMR) AF: 0.393 AC: 5980 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1999 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1823 AN: 5132

South Asian (SAS) AF: 0.461 AC: 2217 AN: 4810

European-Finnish (FIN) AF: 0.484 AC: 5093 AN: 10522

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35032 AN: 67884

Other (OTH) AF: 0.455 AC: 960 AN: 2110

Alfa AF: 0.475 Hom.: 22922

Bravo AF: 0.413

Asia WGS AF: 0.349 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs1558789; hg19: chr12-15168791;