Genetic Variant WDR12:c.*256A>G (chr2-202880604-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018256.4(WDR12):c.*256A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 223,008 control chromosomes in the GnomAD database, including 1,223 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 0.089 ( 739 hom., cov: 32)

Exomes 𝑓: 0.099 ( 484 hom. )

Consequence

WDR12
NM_018256.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.237

Publications

16 publications found

Variant links:

Genes affected

WDR12 (HGNC:14098): (WD repeat domain 12) 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 protein is highly similar to the mouse WD repeat domain 12 protein at the amino acid level. The protein encoded by this gene is a component of a nucleolar protein complex that affects maturation of the large ribosomal subunit.[provided by RefSeq, Dec 2008]

WDR12 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR12	NM_018256.4 link	c.*256A>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000261015.5	NP_060726.3	Q9GZL7Q53T99
WDR12	NM_001371664.1 link	c.*256A>G		3_prime_UTR_variant	Exon 12 of 12		NP_001358593.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
WDR12	ENST00000261015.5 link	c.*256A>G	3_prime_UTR_variant	Exon 13 of 13	1	NM_018256.4	ENSP00000261015.4	Q9GZL7
WDR12	ENST00000467777.1 link	n.479A>G	non_coding_transcript_exon_variant	Exon 2 of 2	2
WDR12	ENST00000688520.1 link	c.*256A>G	3_prime_UTR_variant	Exon 13 of 13			ENSP00000509107.1	Q9GZL7

Frequencies

GnomAD3 genomes

AF:

0.0887

AC:

13440

AN:

151572

Hom.:

734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0324

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.0956

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.0146

Gnomad SAS

AF:

0.0304

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.123

GnomAD4 exome

AF:

0.0992

AC:

7074

AN:

71322

Hom.:

484

Cov.:

AF XY:

0.0982

AC XY:

3652

AN XY:

37188

show subpopulations

African (AFR)

AF:

0.0246

AC:

AN:

1992

American (AMR)

AF:

0.0865

AC:

200

AN:

2312

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

267

AN:

2518

East Asian (EAS)

AF:

0.00908

AC:

AN:

5288

South Asian (SAS)

AF:

0.0357

AC:

137

AN:

3840

European-Finnish (FIN)

AF:

0.109

AC:

471

AN:

4310

Middle Eastern (MID)

AF:

0.116

AC:

AN:

302

European-Non Finnish (NFE)

AF:

0.117

AC:

5386

AN:

46188

Other (OTH)

AF:

0.105

AC:

481

AN:

4572

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

328

655

983

1310

1638

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0887

AC:

13461

AN:

151686

Hom.:

739

Cov.:

AF XY:

0.0859

AC XY:

6365

AN XY:

74128

show subpopulations

African (AFR)

AF:

0.0325

AC:

1346

AN:

41410

American (AMR)

AF:

0.0955

AC:

1454

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

387

AN:

3462

East Asian (EAS)

AF:

0.0147

AC:

AN:

5178

South Asian (SAS)

AF:

0.0307

AC:

147

AN:

4792

European-Finnish (FIN)

AF:

0.105

AC:

1100

AN:

10448

Middle Eastern (MID)

AF:

0.0925

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.125

AC:

8465

AN:

67854

Other (OTH)

AF:

0.130

AC:

274

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

645

1290

1934

2579

3224

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.115

Hom.:

1426

Bravo

AF:

0.0874

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.5

(source)

DANN

Benign

0.75

PhyloP100

0.24

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over