12-130922632-A-G

Variant names:

• chr12-130922632-A-G
• rs4759802

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 0.819 in 152,092 control chromosomes in the GnomAD database, including 51,594 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 0.82 (51594 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124441 AN: 151974 Hom.: 51556 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.819 AC: 124527 AN: 152092 Hom.: 51594 Cov.: 31 AF XY: 0.822 AC XY: 61092 AN XY: 74322

African (AFR) AF: 0.671 AC: 27818 AN: 41450

American (AMR) AF: 0.867 AC: 13262 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2966 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4665 AN: 5172

South Asian (SAS) AF: 0.924 AC: 4454 AN: 4818

European-Finnish (FIN) AF: 0.852 AC: 9008 AN: 10576

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59611 AN: 68000

Other (OTH) AF: 0.821 AC: 1733 AN: 2112

Alfa AF: 0.838 Hom.: 22399

Bravo AF: 0.813

Asia WGS AF: 0.887 AC: 3086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs4759802; hg19: chr12-131407177;