chr15-55830589-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006154.4(NEDD4):c.2528-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,613,636 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006154.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEDD4 | NM_006154.4 | c.2528-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000435532.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEDD4 | ENST00000435532.8 | c.2528-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006154.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000406 AC: 102AN: 251372Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135860
GnomAD4 exome AF: 0.000187 AC: 273AN: 1461312Hom.: 4 Cov.: 30 AF XY: 0.000264 AC XY: 192AN XY: 727030
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at