chr12-87590195-G-A

Variant names:

• chr12-87590195-G-A
• rs790428

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 0.0783 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.229 AC: 9479 AN: 41448

American (AMR) AF: 0.0332 AC: 505 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0335 AC: 116 AN: 3466

East Asian (EAS) AF: 0.00253 AC: 13 AN: 5136

South Asian (SAS) AF: 0.0158 AC: 76 AN: 4824

European-Finnish (FIN) AF: 0.00802 AC: 85 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0214 AC: 1451 AN: 67892

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0612 Hom.: 123

Bravo AF: 0.0884

Asia WGS AF: 0.0250 AC: 85 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.13
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs790428; hg19: chr12-87983972;