rs12063142

Variant names:

• chr1-18813023-C-T
• rs12063142

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 0.28 in 151,860 control chromosomes in the GnomAD database, including 6,312 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 0.28 (6312 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42551 AN: 151742 Hom.: 6305 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.280 AC: 42566 AN: 151860 Hom.: 6312 Cov.: 31 AF XY: 0.283 AC XY: 20980 AN XY: 74202

African (AFR) AF: 0.256 AC: 10618 AN: 41404

American (AMR) AF: 0.286 AC: 4358 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3472

East Asian (EAS) AF: 0.0369 AC: 190 AN: 5144

South Asian (SAS) AF: 0.365 AC: 1752 AN: 4802

European-Finnish (FIN) AF: 0.350 AC: 3676 AN: 10508

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20029 AN: 67970

Other (OTH) AF: 0.271 AC: 571 AN: 2104

Alfa AF: 0.282 Hom.: 15956

Bravo AF: 0.268

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.025
DANN	Benign	0.56
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs12063142; hg19: chr1-19139517;