rs12425131

Variant names:

• chr12-82591100-G-A
• rs12425131

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 0.0531 in 152,090 control chromosomes in the GnomAD database, including 342 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 0.053 (342 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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: 0.0531 AC: 8076 AN: 151970 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0531 AC: 8083 AN: 152090 Hom.: 342 Cov.: 32 AF XY: 0.0544 AC XY: 4046 AN XY: 74364

African (AFR) AF: 0.0956 AC: 3966 AN: 41478

American (AMR) AF: 0.0686 AC: 1046 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3466

East Asian (EAS) AF: 0.165 AC: 855 AN: 5168

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4822

European-Finnish (FIN) AF: 0.0205 AC: 217 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0218 AC: 1483 AN: 67998

Other (OTH) AF: 0.0456 AC: 96 AN: 2106

Alfa AF: 0.0330 Hom.: 302

Bravo AF: 0.0583

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs12425131; hg19: chr12-82984879;