rs12814605

Variant names:

• chr12-63044365-C-T
• rs12814605

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 0.104 in 152,204 control chromosomes in the GnomAD database, including 978 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 0.10 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

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 (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.104 AC: 15819 AN: 152086 Hom.: 980 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.104 AC: 15823 AN: 152204 Hom.: 978 Cov.: 32 AF XY: 0.106 AC XY: 7922 AN XY: 74422

Gnomad4 AFR AF: 0.0699

Gnomad4 AMR AF: 0.0882

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.0796

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.101

Alfa AF: 0.121 Hom.: 1544

Bravo AF: 0.0946

Asia WGS AF: 0.0470 AC: 165 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	2.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12814605; hg19: chr12-63438145;