5-111107529-C-T

Position:

• chr5-111107529-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.1326+90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 1,517,830 control chromosomes in the GnomAD database, including 180,361 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 0.54 (22693 hom., cov: 32)
  • Exomes 𝑓: 0.47 (157668 hom.)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

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]

WDR36 (HGNC:):

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 = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR36	NM_139281.3	c.1326+90C>T		intron_variant		ENST00000513710.4	NP_644810.2
WDR36	XM_047416729.1	c.1326+90C>T		intron_variant			XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR36	ENST00000513710.4	c.1326+90C>T		intron_variant		1	NM_139281.3	ENSP00000424628.3
WDR36	ENST00000505303.5	n.1462+90C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81212 AN: 150958 Hom.: 22662 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 0.474 AC: 647377 AN: 1366754 Hom.: 157668 AF XY: 0.479 AC XY: 325749 AN XY: 679524

Gnomad4 AFR exome AF: 0.677

Gnomad4 AMR exome AF: 0.623

Gnomad4 ASJ exome AF: 0.495

Gnomad4 EAS exome AF: 0.361

Gnomad4 SAS exome AF: 0.678

Gnomad4 FIN exome AF: 0.528

Gnomad4 NFE exome AF: 0.447

Gnomad4 OTH exome AF: 0.488

GnomAD4 genome AF: 0.538 AC: 81299 AN: 151076 Hom.: 22693 Cov.: 32 AF XY: 0.544 AC XY: 40160 AN XY: 73838

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.527

Alfa AF: 0.513 Hom.: 2636

Bravo AF: 0.536

Asia WGS AF: 0.530 AC: 1845 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.25

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: rs10043631; hg19: chr5-110443228;