rs1015142

Positions:

• chr20-12084345-C-A

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 0.0746 in 152,206 control chromosomes in the GnomAD database, including 1,158 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 0.075 (1158 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12084345C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0743 AC: 11303 AN: 152088 Hom.: 1139 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00960

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0746 AC: 11359 AN: 152206 Hom.: 1158 Cov.: 32 AF XY: 0.0736 AC XY: 5477 AN XY: 74428

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0338

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0803

Gnomad4 FIN AF: 0.000753

Gnomad4 NFE AF: 0.00961

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0194 Hom.: 267

Bravo AF: 0.0832

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015142; hg19: chr20-12064993;