rs1043828

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_139281.3(WDR36):​c.*1427T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 185,036 control chromosomes in the GnomAD database, including 7,751 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 0.26 ( 6206 hom., cov: 31)
Exomes 𝑓: 0.28 ( 1545 hom. )

Consequence

WDR36
NM_139281.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02
Variant links:
Genes affected
WDR36 (HGNC:30696): (WD repeat domain 36) 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. Mutations in this gene have been associated with adult-onset primary open-angle glaucoma (POAG). [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR36NM_139281.3 linkuse as main transcriptc.*1427T>C 3_prime_UTR_variant 23/23 ENST00000513710.4 NP_644810.2 Q8NI36

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR36ENST00000513710.4 linkuse as main transcriptc.*1427T>C 3_prime_UTR_variant 23/231 NM_139281.3 ENSP00000424628.3 A0A0A0MTB8

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
39978
AN:
151800
Hom.:
6206
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.134
Gnomad AMI
AF:
0.468
Gnomad AMR
AF:
0.288
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.0430
Gnomad SAS
AF:
0.104
Gnomad FIN
AF:
0.294
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.352
Gnomad OTH
AF:
0.286
GnomAD4 exome
AF:
0.278
AC:
9196
AN:
33118
Hom.:
1545
Cov.:
0
AF XY:
0.281
AC XY:
4289
AN XY:
15256
show subpopulations
Gnomad4 AFR exome
AF:
0.136
Gnomad4 AMR exome
AF:
0.254
Gnomad4 ASJ exome
AF:
0.337
Gnomad4 EAS exome
AF:
0.0450
Gnomad4 SAS exome
AF:
0.0828
Gnomad4 FIN exome
AF:
0.438
Gnomad4 NFE exome
AF:
0.354
Gnomad4 OTH exome
AF:
0.329
GnomAD4 genome
AF:
0.263
AC:
39988
AN:
151918
Hom.:
6206
Cov.:
31
AF XY:
0.255
AC XY:
18951
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.134
Gnomad4 AMR
AF:
0.288
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.0429
Gnomad4 SAS
AF:
0.104
Gnomad4 FIN
AF:
0.294
Gnomad4 NFE
AF:
0.352
Gnomad4 OTH
AF:
0.286
Alfa
AF:
0.333
Hom.:
17789
Bravo
AF:
0.264
Asia WGS
AF:
0.112
AC:
388
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
3.1
DANN
Benign
0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1043828; hg19: chr5-110464008; API