1-108974551-C-T
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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
NM_001142551.2 missense
Scores
4
10
5
Clinical Significance
Conservation
PhyloP100: 4.63
Genes affected
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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 |
---|---|---|---|---|---|---|---|---|
WDR47 | NM_001142551.2 | c.2602G>A | p.Val868Met | missense_variant | 14/15 | ENST00000369962.8 | NP_001136023.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDR47 | ENST00000369962.8 | c.2602G>A | p.Val868Met | missense_variant | 14/15 | 1 | NM_001142551.2 | ENSP00000358979.3 | ||
WDR47 | ENST00000400794.7 | c.2626G>A | p.Val876Met | missense_variant | 14/15 | 1 | ENSP00000383599.3 | |||
WDR47 | ENST00000369965.8 | c.2605G>A | p.Val869Met | missense_variant | 14/15 | 1 | ENSP00000358982.4 | |||
WDR47 | ENST00000361054.7 | c.2518G>A | p.Val840Met | missense_variant | 13/14 | 5 | ENSP00000354339.3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250684Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135520
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461756Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727162
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74326
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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 submitter | clinical testing | Ambry Genetics | Oct 01, 2024 | The 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.;T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
.;L;.;.;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;.
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;.
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.98, 0.95, 0.90
.;D;P;P;.
Vest4
MutPred
0.62
.;Loss of methylation at K867 (P = 0.0384);.;.;.;
MVP
MPC
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at