rs12823849

chr12-63015847-T-C

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 0.0735 in 152,158 control chromosomes in the GnomAD database, including 464 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 0.074 (464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 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: 0.0735 AC: 11179 AN: 152040 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0735 AC: 11190 AN: 152158 Hom.: 464 Cov.: 32 AF XY: 0.0735 AC XY: 5471 AN XY: 74406

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0854 Hom.: 514

Bravo AF: 0.0724

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.8
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: rs12823849; hg19: chr12-63409627;