chr7-4788227-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_014855.3(AP5Z1):c.1528C>A(p.Arg510=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000703 in 1,421,620 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R510R) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP5Z1 | NM_014855.3 | c.1528C>A | p.Arg510= | synonymous_variant | 12/17 | ENST00000649063.2 | |
AP5Z1 | NM_001364858.1 | c.1060C>A | p.Arg354= | synonymous_variant | 11/16 | ||
AP5Z1 | XM_047421098.1 | c.1192C>A | p.Arg398= | synonymous_variant | 10/15 | ||
AP5Z1 | NR_157345.1 | n.1659C>A | non_coding_transcript_exon_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5Z1 | ENST00000649063.2 | c.1528C>A | p.Arg510= | synonymous_variant | 12/17 | NM_014855.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000108 AC: 2AN: 185682Hom.: 0 AF XY: 0.00000997 AC XY: 1AN XY: 100344
GnomAD4 exome AF: 7.03e-7 AC: 1AN: 1421620Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 703662
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at