GeneBe

rs16975963

Variant names:

Variant summary

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

The ENST00000592640.6(WDR87BP):​n.303-1382G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,594 control chromosomes in the GnomAD database, including 4,694 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 0.25 ( 4694 hom., cov: 30)

Consequence

WDR87BP
ENST00000592640.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.231

Publications

17 publications found
Variant links:
Genes affected
WDR87BP (HGNC:55125): (WD repeat domain 87B, pseudogene)

Genome browser will be placed here

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=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
WDR87BPNR_040015.1 linkn.281-1382G>C intron_variant Intron 3 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
WDR87BPENST00000592640.6 linkn.303-1382G>C intron_variant Intron 3 of 5 1
WDR87BPENST00000433142.6 linkn.356-1382G>C intron_variant Intron 3 of 3 3
WDR87BPENST00000587395.6 linkn.502-1382G>C intron_variant Intron 3 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.248
AC:
37584
AN:
151474
Hom.:
4686
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.277
Gnomad AMI
AF:
0.268
Gnomad AMR
AF:
0.283
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.288
Gnomad SAS
AF:
0.238
Gnomad FIN
AF:
0.262
Gnomad MID
AF:
0.309
Gnomad NFE
AF:
0.216
Gnomad OTH
AF:
0.256
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.248
AC:
37615
AN:
151594
Hom.:
4694
Cov.:
30
AF XY:
0.252
AC XY:
18655
AN XY:
74074
show subpopulations
African (AFR)
AF:
0.276
AC:
11427
AN:
41330
American (AMR)
AF:
0.284
AC:
4314
AN:
15214
Ashkenazi Jewish (ASJ)
AF:
0.282
AC:
976
AN:
3462
East Asian (EAS)
AF:
0.288
AC:
1476
AN:
5126
South Asian (SAS)
AF:
0.238
AC:
1143
AN:
4796
European-Finnish (FIN)
AF:
0.262
AC:
2744
AN:
10458
Middle Eastern (MID)
AF:
0.310
AC:
91
AN:
294
European-Non Finnish (NFE)
AF:
0.216
AC:
14653
AN:
67896
Other (OTH)
AF:
0.260
AC:
547
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1409
2818
4227
5636
7045
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
388
776
1164
1552
1940
<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:
0.210
Hom.:
1917
Bravo
AF:
0.255
Asia WGS
AF:
0.273
AC:
948
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.4
DANN
Benign
0.51
PhyloP100
-0.23

Splicing

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

Publications

Other links and lift over

dbSNP: rs16975963; hg19: chr19-38325536; COSMIC: COSV70465428; API