rs185533207
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001144967.3(NEDD4L):c.535T>A(p.Ser179Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001144967.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEDD4L | NM_001144967.3 | c.535T>A | p.Ser179Thr | missense_variant | 9/31 | ENST00000400345.8 | NP_001138439.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEDD4L | ENST00000400345.8 | c.535T>A | p.Ser179Thr | missense_variant | 9/31 | 1 | NM_001144967.3 | ENSP00000383199.2 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000498 AC: 124AN: 249078Hom.: 0 AF XY: 0.000407 AC XY: 55AN XY: 135098
GnomAD4 exome AF: 0.000471 AC: 688AN: 1461568Hom.: 0 Cov.: 31 AF XY: 0.000499 AC XY: 363AN XY: 727056
GnomAD4 genome AF: 0.000499 AC: 76AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 27, 2020 | This variant is associated with the following publications: (PMID: 27694961) - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 05, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | NEDD4L: BS1 - |
Periventricular nodular heterotopia 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at