19-36101683-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The ENST00000401500.7(WDR62):c.2991C>A(p.Ala997Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,550,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A997A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
WDR62
ENST00000401500.7 synonymous
ENST00000401500.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.43
Publications
4 publications found
Genes affected
WDR62 (HGNC:24502): (WD repeat domain 62) This gene is proposed to play a role in cerebral cortical development. Mutations in this gene have been associated with microencephaly, cortical malformations, and cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2011]
WDR62 Gene-Disease associations (from GenCC):
- microcephaly 2, primary, autosomal recessive, with or without cortical malformationsInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, Illumina, G2P, ClinGen
- autosomal recessive primary microcephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP7
Synonymous conserved (PhyloP=-1.43 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000401500.7. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WDR62 | NM_001083961.2 | MANE Select | c.2991C>A | p.Ala997Ala | synonymous | Exon 25 of 32 | NP_001077430.1 | ||
| WDR62 | NM_001411145.1 | c.2976C>A | p.Ala992Ala | synonymous | Exon 25 of 32 | NP_001398074.1 | |||
| WDR62 | NM_173636.5 | c.2991C>A | p.Ala997Ala | synonymous | Exon 25 of 32 | NP_775907.4 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| WDR62 | ENST00000401500.7 | TSL:1 MANE Select | c.2991C>A | p.Ala997Ala | synonymous | Exon 25 of 32 | ENSP00000384792.1 | ||
| WDR62 | ENST00000587391.6 | TSL:1 | n.*2027C>A | non_coding_transcript_exon | Exon 25 of 30 | ENSP00000465525.1 | |||
| WDR62 | ENST00000587391.6 | TSL:1 | n.*2027C>A | 3_prime_UTR | Exon 25 of 30 | ENSP00000465525.1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152138
Hom.:
Cov.:
33
Gnomad AFR
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GnomAD2 exomes AF: 0.00000646 AC: 1AN: 154824 AF XY: 0.0000122 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
154824
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00000143 AC: 2AN: 1398706Hom.: 0 Cov.: 32 AF XY: 0.00000290 AC XY: 2AN XY: 689886 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1398706
Hom.:
Cov.:
32
AF XY:
AC XY:
2
AN XY:
689886
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31594
American (AMR)
AF:
AC:
0
AN:
35704
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25180
East Asian (EAS)
AF:
AC:
0
AN:
35742
South Asian (SAS)
AF:
AC:
1
AN:
79234
European-Finnish (FIN)
AF:
AC:
0
AN:
48682
Middle Eastern (MID)
AF:
AC:
0
AN:
5648
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1078924
Other (OTH)
AF:
AC:
0
AN:
57998
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
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2
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74312 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152138
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74312
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41432
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5188
South Asian (SAS)
AF:
AC:
0
AN:
4822
European-Finnish (FIN)
AF:
AC:
0
AN:
10614
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68014
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
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0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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