rs1558789

Variant names:

• chr12-15015857-C-A
• rs1558789

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 0.429 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.429 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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.455

Alfa AF: 0.505 Hom.: 16193

Bravo AF: 0.413

Asia WGS AF: 0.349 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558789; hg19: chr12-15168791;