2-202991734-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000477723.1(WDR12):n.242+22823T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,274 control chromosomes in the GnomAD database, including 58,821 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 0.88 (58821 hom., cov: 34)
• Consequence: WDR12 ENST00000477723.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

Genes affected

WDR12 (HGNC:14098): (WD repeat domain 12) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein is highly similar to the mouse WD repeat domain 12 protein at the amino acid level. The protein encoded by this gene is a component of a nucleolar protein complex that affects maturation of the large ribosomal subunit.[provided by RefSeq, Dec 2008]

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 = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR12	ENST00000477723.1	n.242+22823T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133180 AN: 152156 Hom.: 58781 Cov.: 34

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.875 AC: 133271 AN: 152274 Hom.: 58821 Cov.: 34 AF XY: 0.878 AC XY: 65372 AN XY: 74458

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.938

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.888

Alfa AF: 0.913 Hom.: 84610

Bravo AF: 0.860

Asia WGS AF: 0.919 AC: 3195 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	2.6
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1864466; hg19: chr2-203856457;