rs10038058

chr5-111107582-A-Gchr5-111107582-A-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.1326+143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,052,140 control chromosomes in the GnomAD database, including 124,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (22726 hom., cov: 32)
  • Exomes 𝑓: 0.47 (101604 hom.)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.60

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=-1.02).
• BP6: Variant 5-111107582-A-G is Benign according to our data. Variant chr5-111107582-A-G is described in ClinVar as [Benign]. Clinvar id is 1287637.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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	UniProt
WDR36	NM_139281.3	c.1326+143A>G		intron_variant		ENST00000513710.4
WDR36	XM_047416729.1	c.1326+143A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR36	ENST00000513710.4	c.1326+143A>G		intron_variant		1	NM_139281.3	P1
WDR36	ENST00000505303.5	n.1462+143A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81256 AN: 150972 Hom.: 22695 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.364

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: 0.643

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 0.465 AC: 419170 AN: 901050 Hom.: 101604 AF XY: 0.473 AC XY: 216822 AN XY: 457946

Gnomad4 AFR exome AF: 0.666

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.488

Gnomad4 EAS exome AF: 0.355

Gnomad4 SAS exome AF: 0.677

Gnomad4 FIN exome AF: 0.523

Gnomad4 NFE exome AF: 0.437

Gnomad4 OTH exome AF: 0.481

GnomAD4 genome AF: 0.538 AC: 81343 AN: 151090 Hom.: 22726 Cov.: 32 AF XY: 0.544 AC XY: 40186 AN XY: 73848

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.527

Alfa AF: 0.518 Hom.: 3632

Bravo AF: 0.537

Asia WGS AF: 0.535 AC: 1862 AN: 3476

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

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs10038058; hg19: chr5-110443281;