rs12813083

chr12-62974950-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;