rs12023000

Variant names:

• chr1-20463152-A-G
• rs12023000

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 0.0766 in 152,116 control chromosomes in the GnomAD database, including 532 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 0.077 (532 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.716
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.21 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: 0.0765 AC: 11624 AN: 151998 Hom.: 526 Cov.: 30

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0534

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0766 AC: 11657 AN: 152116 Hom.: 532 Cov.: 30 AF XY: 0.0788 AC XY: 5858 AN XY: 74338

African (AFR) AF: 0.0835 AC: 3466 AN: 41492

American (AMR) AF: 0.0533 AC: 816 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1132 AN: 5126

South Asian (SAS) AF: 0.137 AC: 661 AN: 4816

European-Finnish (FIN) AF: 0.0720 AC: 763 AN: 10594

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0664 AC: 4517 AN: 67998

Other (OTH) AF: 0.0878 AC: 185 AN: 2108

Alfa AF: 0.0730 Hom.: 718

Bravo AF: 0.0738

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.76
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs12023000; hg19: chr1-20789645;