rs790428

Variant names:

• chr12-87590195-G-A
• rs790428

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 0.0783 in 151,884 control chromosomes in the GnomAD database, including 1,137 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 0.078 (1137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.0781 AC: 11847 AN: 151768 Hom.: 1128 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0332

Gnomad ASJ AF: 0.0335

Gnomad EAS AF: 0.00253

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.00802

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0783 AC: 11893 AN: 151884 Hom.: 1137 Cov.: 32 AF XY: 0.0757 AC XY: 5617 AN XY: 74220

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0335

Gnomad4 EAS AF: 0.00253

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.00802

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0563 Hom.: 105

Bravo AF: 0.0884

Asia WGS AF: 0.0250 AC: 85 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs790428; hg19: chr12-87983972;