1-108974551-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001142551.2(WDR47):​c.2602G>A​(p.Val868Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

WDR47
NM_001142551.2 missense

Scores

4
10
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.63
Variant links:
Genes affected
WDR47 (HGNC:29141): (WD repeat domain 47) Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WDR47NM_001142551.2 linkuse as main transcriptc.2602G>A p.Val868Met missense_variant 14/15 ENST00000369962.8 NP_001136023.1 O94967-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WDR47ENST00000369962.8 linkuse as main transcriptc.2602G>A p.Val868Met missense_variant 14/151 NM_001142551.2 ENSP00000358979.3 O94967-1
WDR47ENST00000400794.7 linkuse as main transcriptc.2626G>A p.Val876Met missense_variant 14/151 ENSP00000383599.3 O94967-4
WDR47ENST00000369965.8 linkuse as main transcriptc.2605G>A p.Val869Met missense_variant 14/151 ENSP00000358982.4 O94967-3
WDR47ENST00000361054.7 linkuse as main transcriptc.2518G>A p.Val840Met missense_variant 13/145 ENSP00000354339.3 O94967-2

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152152
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
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
GnomAD3 exomes
AF:
0.00000399
AC:
1
AN:
250684
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135520
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461756
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727162
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152152
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 01, 2024The c.2626G>A (p.V876M) alteration is located in exon 14 (coding exon 13) of the WDR47 gene. This alteration results from a G to A substitution at nucleotide position 2626, causing the valine (V) at amino acid position 876 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Pathogenic
0.14
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.089
.;T;.;.;T
Eigen
Uncertain
0.68
Eigen_PC
Pathogenic
0.66
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Uncertain
0.96
D;D;D;D;D
M_CAP
Benign
0.062
D
MetaRNN
Uncertain
0.58
D;D;D;D;D
MetaSVM
Uncertain
-0.27
T
MutationAssessor
Benign
1.7
.;L;.;.;.
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-0.23
N;N;N;N;.
REVEL
Uncertain
0.38
Sift
Uncertain
0.0080
D;D;D;D;.
Sift4G
Uncertain
0.036
D;D;D;D;D
Polyphen
0.98, 0.95, 0.90
.;D;P;P;.
Vest4
0.68
MutPred
0.62
.;Loss of methylation at K867 (P = 0.0384);.;.;.;
MVP
0.57
MPC
2.0
ClinPred
0.86
D
GERP RS
5.3
Varity_R
0.24
gMVP
0.31

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

LitVar

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

Other links and lift over

dbSNP: rs752386856; hg19: chr1-109517173; API