7-4784361-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_014855.3(AP5Z1):c.780C>T(p.Thr260Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T260T) has been classified as Likely benign.
Frequency
Consequence
NM_014855.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP5Z1 | NM_014855.3 | c.780C>T | p.Thr260Thr | synonymous_variant | 6/17 | ENST00000649063.2 | NP_055670.1 | |
AP5Z1 | NM_001364858.1 | c.312C>T | p.Thr104Thr | synonymous_variant | 5/16 | NP_001351787.1 | ||
AP5Z1 | XM_047421098.1 | c.444C>T | p.Thr148Thr | synonymous_variant | 4/15 | XP_047277054.1 | ||
AP5Z1 | NR_157345.1 | n.873C>T | non_coding_transcript_exon_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP5Z1 | ENST00000649063.2 | c.780C>T | p.Thr260Thr | synonymous_variant | 6/17 | NM_014855.3 | ENSP00000497815.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1444820Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0AN XY: 717550
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at