GeneBe

rs139878372

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015910.7(WDPCP):​c.*612_*625delAAAAAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000069 ( 0 hom., cov: 0)

Consequence

WDPCP
NM_015910.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

0 publications found
Variant links:
Genes affected
WDPCP (HGNC:28027): (WD repeat containing planar cell polarity effector) This gene encodes a cytoplasmic WD40 repeat protein. A similar gene in frogs encodes a planar cell polarity protein that plays a critical role in collective cell movement and ciliogenesis by mediating septin localization. Mutations in this gene are associated with Bardet-Biedl syndrome 15 and may also play a role in Meckel-Gruber syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
WDPCP Gene-Disease associations (from GenCC):
  • Bardet-Biedl syndrome 15
    Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • ciliopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • Bardet-Biedl syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • heart defect - tongue hamartoma - polysyndactyly syndrome
    Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015910.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
WDPCP
NM_015910.7
MANE Select
c.*612_*625delAAAAAAAAAAAAAA
3_prime_UTR
Exon 18 of 18NP_056994.3O95876-1
WDPCP
NM_001354044.2
c.*612_*625delAAAAAAAAAAAAAA
3_prime_UTR
Exon 19 of 19NP_001340973.1
WDPCP
NM_001042692.3
c.*612_*625delAAAAAAAAAAAAAA
3_prime_UTR
Exon 12 of 12NP_001036157.1O95876-3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
WDPCP
ENST00000272321.12
TSL:1 MANE Select
c.*612_*625delAAAAAAAAAAAAAA
3_prime_UTR
Exon 18 of 18ENSP00000272321.7O95876-1
WDPCP
ENST00000946853.1
c.*612_*625delAAAAAAAAAAAAAA
splice_region
Exon 14 of 14ENSP00000616912.1
WDPCP
ENST00000872046.1
c.*612_*625delAAAAAAAAAAAAAA
3_prime_UTR
Exon 18 of 18ENSP00000542105.1

Frequencies

GnomAD3 genomes
AF:
0.0000687
AC:
6
AN:
87316
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000219
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000320
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000687
AC:
6
AN:
87304
Hom.:
0
Cov.:
0
AF XY:
0.0000991
AC XY:
4
AN XY:
40344
show subpopulations
African (AFR)
AF:
0.000218
AC:
5
AN:
22884
American (AMR)
AF:
0.00
AC:
0
AN:
7456
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2472
East Asian (EAS)
AF:
0.000321
AC:
1
AN:
3114
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2438
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2778
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
156
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
44310
Other (OTH)
AF:
0.00
AC:
0
AN:
1118
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.667
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<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:
0.00
Hom.:
481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs139878372; hg19: chr2-63348515; API