12-13391129-G-A

Variant names:

• chr12-13391129-G-A
• rs12580476

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 0.0991 in 152,152 control chromosomes in the GnomAD database, including 956 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 0.099 (956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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: 0.0992 AC: 15083 AN: 152034 Hom.: 957 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0991 AC: 15073 AN: 152152 Hom.: 956 Cov.: 32 AF XY: 0.0987 AC XY: 7339 AN XY: 74386

African (AFR) AF: 0.0255 AC: 1059 AN: 41512

American (AMR) AF: 0.0817 AC: 1248 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.0613 AC: 318 AN: 5186

South Asian (SAS) AF: 0.110 AC: 532 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10574

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9952 AN: 68002

Other (OTH) AF: 0.101 AC: 213 AN: 2108

Alfa AF: 0.125 Hom.: 723

Bravo AF: 0.0915

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.69
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12580476; hg19: chr12-13544063;