15-55847024-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006154.4(NEDD4):āc.1553A>Gā(p.Tyr518Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,454,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006154.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEDD4 | NM_006154.4 | c.1553A>G | p.Tyr518Cys | missense_variant | 18/29 | ENST00000435532.8 | NP_006145.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEDD4 | ENST00000435532.8 | c.1553A>G | p.Tyr518Cys | missense_variant | 18/29 | 1 | NM_006154.4 | ENSP00000410613.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248290Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134024
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1454276Hom.: 0 Cov.: 28 AF XY: 0.00000276 AC XY: 2AN XY: 723496
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2024 | The c.2594A>G (p.Y865C) alteration is located in exon 11 (coding exon 11) of the NEDD4 gene. This alteration results from a A to G substitution at nucleotide position 2594, causing the tyrosine (Y) at amino acid position 865 to be replaced by a cysteine (C). 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