rs12814605

Variant names:

• chr12-63044365-C-T
• rs12814605

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0699 AC: 2905 AN: 41532

American (AMR) AF: 0.0882 AC: 1350 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5170

South Asian (SAS) AF: 0.0796 AC: 384 AN: 4826

European-Finnish (FIN) AF: 0.186 AC: 1973 AN: 10584

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8531 AN: 68000

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.118 Hom.: 1903

Bravo AF: 0.0946

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.71
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12814605; hg19: chr12-63438145;