chr14-102143256-C-T

Variant names:

• chr14-102143256-C-T
• rs1190584
• NM_144574.4:c.249+3084C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144574.4(WDR20):​c.249+3084C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,052 control chromosomes in the GnomAD database, including 36,266 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 0.66 (36266 hom., cov: 32)
• Consequence: WDR20 NM_144574.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 6 publications found

Genes affected

WDR20 (HGNC:19667): (WD repeat domain 20) This gene encodes a WD repeat-containing protein that functions to preserve and regulate the activity of the USP12-UAF1 deubiquitinating enzyme complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR20	NM_144574.4	c.249+3084C>T		intron_variant	Intron 1 of 2	ENST00000342702.8	NP_653175.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR20	ENST00000342702.8	c.249+3084C>T		intron_variant	Intron 1 of 2	1	NM_144574.4	ENSP00000341037.3

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99758 AN: 151934 Hom.: 36258 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.656 AC: 99787 AN: 152052 Hom.: 36266 Cov.: 32 AF XY: 0.662 AC XY: 49189 AN XY: 74320

African (AFR) AF: 0.312 AC: 12936 AN: 41452

American (AMR) AF: 0.777 AC: 11875 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3470

East Asian (EAS) AF: 0.923 AC: 4789 AN: 5186

South Asian (SAS) AF: 0.745 AC: 3580 AN: 4808

European-Finnish (FIN) AF: 0.757 AC: 7991 AN: 10556

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53462 AN: 67988

Other (OTH) AF: 0.678 AC: 1430 AN: 2110

Alfa AF: 0.691 Hom.: 7617

Bravo AF: 0.644

Asia WGS AF: 0.810 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.79
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1190584; hg19: chr14-102609593;