Genetic Variant WDR11:c.*557G>T (chr10-120909270-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018117.12(WDR11):c.*557G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 154,886 control chromosomes in the GnomAD database, including 7,777 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 0.31 ( 7629 hom., cov: 33)

Exomes 𝑓: 0.30 ( 148 hom. )

Consequence

WDR11
NM_018117.12 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.861

Publications

8 publications found

Variant links:

Genes affected

WDR11 (HGNC:13831): (WD repeat domain 11) 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. This gene is located in the chromosome 10q25-26 region, which is frequently deleted in gliomas and tumors of other tissues, and is disrupted by the t(10;19) translocation rearrangement in glioblastoma cells. The gene location suggests that it is a candidate gene for the tumor suppressor locus. [provided by RefSeq, Jul 2008]

WDR11 Gene-Disease associations (from GenCC):

hypogonadotropic hypogonadism 14 with or without anosmia
Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Illumina, Labcorp Genetics (formerly Invitae)
intellectual developmental disorder, autosomal recessive 78
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
hypogonadotropic hypogonadism
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Kallmann syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

WDR11 links:

LOC105378519 (HGNC:):

LOC105378519 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018117.12. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR11	NM_018117.12	MANE Select	c.*557G>T		3_prime_UTR	Exon 29 of 29	NP_060587.8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
WDR11	ENST00000263461.11	TSL:1 MANE Select	c.*557G>T	3_prime_UTR	Exon 29 of 29	ENSP00000263461.5	Q9BZH6
WDR11	ENST00000497136.6	TSL:1	n.*3505G>T	non_coding_transcript_exon	Exon 26 of 26	ENSP00000474595.1	S4R3P9
WDR11	ENST00000497136.6	TSL:1	n.*3505G>T	3_prime_UTR	Exon 26 of 26	ENSP00000474595.1	S4R3P9

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47225

AN:

151654

Hom.:

7623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.381

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.322

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.319

GnomAD4 exome

AF:

0.303

AC:

942

AN:

3114

Hom.:

148

Cov.:

AF XY:

0.295

AC XY:

490

AN XY:

1660

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.353

AC:

201

AN:

570

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.143

AC:

AN:

South Asian (SAS)

AF:

0.257

AC:

AN:

214

European-Finnish (FIN)

AF:

0.280

AC:

115

AN:

410

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.305

AC:

535

AN:

1752

Other (OTH)

AF:

0.240

AC:

AN:

100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

117

146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.311

AC:

47253

AN:

151772

Hom.:

7629

Cov.:

AF XY:

0.311

AC XY:

23039

AN XY:

74150

show subpopulations

African (AFR)

AF:

0.215

AC:

8862

AN:

41252

American (AMR)

AF:

0.415

AC:

6341

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.385

AC:

1337

AN:

3470

East Asian (EAS)

AF:

0.416

AC:

2139

AN:

5146

South Asian (SAS)

AF:

0.332

AC:

1599

AN:

4822

European-Finnish (FIN)

AF:

0.283

AC:

2985

AN:

10544

Middle Eastern (MID)

AF:

0.318

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.337

AC:

22881

AN:

67954

Other (OTH)

AF:

0.317

AC:

670

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1652

3304

4955

6607

8259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.322

Hom.:

2017

Bravo

AF:

0.318

Asia WGS

AF:

0.376

AC:

1308

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.7

(source)

DANN

Benign

0.65

PhyloP100

0.86

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over