5-111099792-C-T

Variant summary

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

The NM_139281.3(WDR36):c.410-797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 151,870 control chromosomes in the GnomAD database, including 1,434 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 0.13 (1434 hom., cov: 31)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

WDR36 (HGNC:30696): (WD repeat domain 36) 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. Mutations in this gene have been associated with adult-onset primary open-angle glaucoma (POAG). [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR36	NM_139281.3	c.410-797C>T		intron_variant		ENST00000513710.4
WDR36	XM_047416729.1	c.410-797C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR36	ENST00000513710.4	c.410-797C>T		intron_variant		1	NM_139281.3	P1
WDR36	ENST00000504122.2	n.292-797C>T		intron_variant, non_coding_transcript_variant		4
WDR36	ENST00000505303.5	n.546-797C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20247 AN: 151752 Hom.: 1435 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.133 AC: 20248 AN: 151870 Hom.: 1434 Cov.: 31 AF XY: 0.135 AC XY: 9986 AN XY: 74232

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.130

Alfa AF: 0.139 Hom.: 3397

Bravo AF: 0.121

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.086
Dann	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416257; hg19: chr5-110435490;