rs13161853

chr5-111111042-C-Achr5-111111042-C-G

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.1607+89C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 1,557,842 control chromosomes in the GnomAD database, including 175,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (20145 hom., cov: 32)
  • Exomes 𝑓: 0.46 (155266 hom.)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.95

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=-0.91).
• BP6: Variant 5-111111042-C-A is Benign according to our data. Variant chr5-111111042-C-A is described in ClinVar as [Benign]. Clinvar id is 1263868.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR36	NM_139281.3	c.1607+89C>A		intron_variant		ENST00000513710.4
WDR36	XM_047416729.1	c.1607+89C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR36	ENST00000513710.4	c.1607+89C>A		intron_variant		1	NM_139281.3	P1
WDR36	ENST00000505303.5	n.1743+89C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.509 AC: 76975 AN: 151214 Hom.: 20119 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.496

GnomAD4 exome AF: 0.463 AC: 650627 AN: 1406510 Hom.: 155266 Cov.: 24 AF XY: 0.469 AC XY: 329436 AN XY: 703026

Gnomad4 AFR exome AF: 0.601

Gnomad4 AMR exome AF: 0.618

Gnomad4 ASJ exome AF: 0.484

Gnomad4 EAS exome AF: 0.357

Gnomad4 SAS exome AF: 0.671

Gnomad4 FIN exome AF: 0.517

Gnomad4 NFE exome AF: 0.435

Gnomad4 OTH exome AF: 0.470

GnomAD4 genome AF: 0.509 AC: 77054 AN: 151332 Hom.: 20145 Cov.: 32 AF XY: 0.516 AC XY: 38117 AN XY: 73916

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.495

Alfa AF: 0.368 Hom.: 1053

Bravo AF: 0.505

Asia WGS AF: 0.524 AC: 1823 AN: 3474

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	-0.91
Cadd	Benign	0.036
Dann	Benign	0.26

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: rs13161853; hg19: chr5-110446741;