dbSNP rs13153937: WDR36:c.292-113G>A (chr5-111098609-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_139281.3(WDR36):c.292-113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 765,734 control chromosomes in the GnomAD database, including 43,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6832 hom., cov: 32)

Exomes 𝑓: 0.33 ( 36619 hom. )

Consequence

WDR36
NM_139281.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.84

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 5-111098609-G-A is Benign according to our data. Variant chr5-111098609-G-A is described in ClinVar as [Benign]. Clinvar id is 1232721.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR36	NM_139281.3 link	c.292-113G>A		intron_variant	Intron 3 of 22	ENST00000513710.4	NP_644810.2	Q8NI36
WDR36	XM_047416729.1 link	c.292-113G>A		intron_variant	Intron 3 of 20		XP_047272685.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WDR36	ENST00000513710.4 link	c.292-113G>A	intron_variant	Intron 3 of 22	1	NM_139281.3	ENSP00000424628.3	A0A0A0MTB8
WDR36	ENST00000504122.2 link	n.174-113G>A	intron_variant	Intron 1 of 4	4
WDR36	ENST00000505303.5 link	n.428-113G>A	intron_variant	Intron 3 of 14	5

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42548

AN:

151854

Hom.:

6823

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.353

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.311

GnomAD4 exome

AF:

0.334

AC:

205281

AN:

613762

Hom.:

36619

AF XY:

0.338

AC XY:

111277

AN XY:

329686

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.366

Gnomad4 EAS exome

AF:

0.311

Gnomad4 SAS exome

AF:

0.409

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.305

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.280

AC:

42559

AN:

151972

Hom.:

6832

Cov.:

AF XY:

0.289

AC XY:

21439

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.132

Gnomad4 AMR

AF:

0.408

Gnomad4 ASJ

AF:

0.353

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.305

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.302

Hom.:

1234

Bravo

AF:

0.276

Asia WGS

AF:

0.338

AC:

1176

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-0.87

CADD

Benign

0.38

DANN

Benign

0.50

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over