rs12063142

Variant names:

• chr1-18813023-C-T
• rs12063142

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 0.28 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.280 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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0369

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.271

Alfa AF: 0.282 Hom.: 11263

Bravo AF: 0.268

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12063142; hg19: chr1-19139517;