chr5-111098675-G-C

Position:

• chr5-111098675-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_139281.3(WDR36):​c.292-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,193,714 control chromosomes in the GnomAD database, including 8 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 0.0019 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0028 (8 hom.)
• Consequence: WDR36 NM_139281.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Homozygotes in GnomAdExome4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR36	NM_139281.3	c.292-47G>C		intron_variant		ENST00000513710.4	NP_644810.2
WDR36	XM_047416729.1	c.292-47G>C		intron_variant			XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR36	ENST00000513710.4	c.292-47G>C		intron_variant		1	NM_139281.3	ENSP00000424628.3
WDR36	ENST00000504122.2	n.174-47G>C		intron_variant		4
WDR36	ENST00000505303.5	n.428-47G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00185 AC: 282 AN: 152098 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000676

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.000459

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000660

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00340

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.00176 AC: 438 AN: 249132 Hom.: 3 AF XY: 0.00168 AC XY: 227 AN XY: 134784

Gnomad AFR exome AF: 0.000498

Gnomad AMR exome AF: 0.000466

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00103

Gnomad NFE exome AF: 0.00342

Gnomad OTH exome AF: 0.00132

GnomAD4 exome AF: 0.00279 AC: 2910 AN: 1041498 Hom.: 8 Cov.: 14 AF XY: 0.00264 AC XY: 1419 AN XY: 537780

Gnomad4 AFR exome AF: 0.000632

Gnomad4 AMR exome AF: 0.000409

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000266

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00108

Gnomad4 NFE exome AF: 0.00367

Gnomad4 OTH exome AF: 0.00306

GnomAD4 genome AF: 0.00185 AC: 282 AN: 152216 Hom.: 0 Cov.: 32 AF XY: 0.00167 AC XY: 124 AN XY: 74416

Gnomad4 AFR AF: 0.000674

Gnomad4 AMR AF: 0.000458

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000660

Gnomad4 NFE AF: 0.00340

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00208 Hom.: 0

Bravo AF: 0.00177

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs34785215; hg19: chr5-110434373;