rs12813083

Variant names:

• chr12-62974950-C-T
• rs12813083

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 0.0755 in 152,178 control chromosomes in the GnomAD database, including 478 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 0.076 (478 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0847 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: 0.0755 AC: 11477 AN: 152060 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0755 AC: 11492 AN: 152178 Hom.: 478 Cov.: 32 AF XY: 0.0750 AC XY: 5579 AN XY: 74408

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.00385

Gnomad4 SAS AF: 0.0572

Gnomad4 FIN AF: 0.0681

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0855 Hom.: 441

Bravo AF: 0.0752

Asia WGS AF: 0.0350 AC: 122 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12813083; hg19: chr12-63368730;