rs12425131

Positions:

• chr12-82591100-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 0.0531 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.0218

Gnomad4 OTH AF: 0.0456

Alfa AF: 0.0283 Hom.: 70

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12425131; hg19: chr12-82984879;