rs12063142

Positions:

• chr1-18813023-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;