rs17554123

chr5-111120810-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_139281.3(WDR36):c.2003-186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 151,850 control chromosomes in the GnomAD database, including 641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.089 (641 hom., cov: 32)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.330

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 5-111120810-C-T is Benign according to our data. Variant chr5-111120810-C-T is described in ClinVar as [Benign]. Clinvar id is 1237174.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR36	NM_139281.3	c.2003-186C>T		intron_variant		ENST00000513710.4
WDR36	XM_047416729.1	c.2003-186C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR36	ENST00000513710.4	c.2003-186C>T		intron_variant		1	NM_139281.3	P1

Frequencies

GnomAD3 genomes AF: 0.0895 AC: 13574 AN: 151732 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.0750

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0905

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0894 AC: 13581 AN: 151850 Hom.: 641 Cov.: 32 AF XY: 0.0921 AC XY: 6833 AN XY: 74190

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.0607

Gnomad4 ASJ AF: 0.0750

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.0815

Alfa AF: 0.0981 Hom.: 96

Bravo AF: 0.0798

Asia WGS AF: 0.151 AC: 523 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.2
Dann	Benign	0.34

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: rs17554123; hg19: chr5-110456508;