13-41072800-T-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_007187.5(WBP4):āc.505T>Gā(p.Trp169Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007187.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WBP4 | NM_007187.5 | c.505T>G | p.Trp169Gly | missense_variant | Exon 7 of 10 | ENST00000379487.5 | NP_009118.1 | |
WBP4 | XM_005266245.3 | c.598T>G | p.Trp200Gly | missense_variant | Exon 7 of 10 | XP_005266302.1 | ||
WBP4 | XM_047430071.1 | c.37T>G | p.Trp13Gly | missense_variant | Exon 2 of 5 | XP_047286027.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250862Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135656
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461386Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727032
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.505T>G (p.W169G) alteration is located in exon 7 (coding exon 7) of the WBP4 gene. This alteration results from a T to G substitution at nucleotide position 505, causing the tryptophan (W) at amino acid position 169 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at