NM_024494.3:c.205C>T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_024494.3(WNT2B):c.205C>T(p.Arg69*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,098 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 Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_024494.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WNT2B | NM_024494.3 | c.205C>T | p.Arg69* | stop_gained | Exon 2 of 5 | ENST00000369684.5 | NP_078613.1 | |
WNT2B | NM_001291880.1 | c.-72C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | NP_001278809.1 | |||
WNT2B | NM_004185.4 | c.148C>T | p.Arg50* | stop_gained | Exon 3 of 6 | NP_004176.2 | ||
WNT2B | NM_001291880.1 | c.-72C>T | 5_prime_UTR_variant | Exon 2 of 5 | NP_001278809.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251468Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135910
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727248
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Diarrhea 9 Pathogenic:1
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Diarrhea;C0401151:Chronic diarrhea;C1867873:Failure to thrive in infancy;C2315100:Failure to thrive;C4476942:Impaired feeding ability Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at