rs790428

chr12-87590195-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;