rs10038058

Variant names:

• chr5-111107582-A-G
• rs10038058
• NM_139281.3:c.1326+143A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-111107582-A-G
• chr5-111107582-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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 Gene-Disease associations (from GenCC):

• glaucoma 1, open angle, G

  Inheritance: Unknown, AD Classification: LIMITED, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
WDR36	NM_139281.3	c.1326+143A>G		intron_variant	Intron 12 of 22	ENST00000513710.4	NP_644810.2
WDR36	XM_047416729.1	c.1326+143A>G		intron_variant	Intron 12 of 20		XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR36	ENST00000513710.4	c.1326+143A>G		intron_variant	Intron 12 of 22	1	NM_139281.3	ENSP00000424628.3
WDR36	ENST00000505303.5	n.1462+143A>G		intron_variant	Intron 12 of 14	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

African (AFR) AF: 0.666 AC: 13265 AN: 19916

American (AMR) AF: 0.607 AC: 13826 AN: 22762

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 9060 AN: 18558

East Asian (EAS) AF: 0.355 AC: 11773 AN: 33134

South Asian (SAS) AF: 0.677 AC: 39421 AN: 58268

European-Finnish (FIN) AF: 0.523 AC: 16936 AN: 32380

Middle Eastern (MID) AF: 0.598 AC: 1726 AN: 2886

European-Non Finnish (NFE) AF: 0.437 AC: 293430 AN: 672116

Other (OTH) AF: 0.481 AC: 19733 AN: 41030

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

African (AFR) AF: 0.672 AC: 27777 AN: 41348

American (AMR) AF: 0.547 AC: 8270 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1700 AN: 3452

East Asian (EAS) AF: 0.394 AC: 2031 AN: 5154

South Asian (SAS) AF: 0.681 AC: 3279 AN: 4816

European-Finnish (FIN) AF: 0.549 AC: 5795 AN: 10562

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 30869 AN: 67334

Other (OTH) AF: 0.527 AC: 1106 AN: 2100

Alfa AF: 0.567 Hom.: 6936

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

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.58
PhyloP100		-2.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10038058; hg19: chr5-110443281;