chr7-4788235-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014855.3(AP5Z1):c.1536G>A(p.Pro512=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000519 in 1,579,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P512P) 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 -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP5Z1 | NM_014855.3 | c.1536G>A | p.Pro512= | synonymous_variant | 12/17 | ENST00000649063.2 | |
AP5Z1 | NM_001364858.1 | c.1068G>A | p.Pro356= | synonymous_variant | 11/16 | ||
AP5Z1 | XM_047421098.1 | c.1200G>A | p.Pro400= | synonymous_variant | 10/15 | ||
AP5Z1 | NR_157345.1 | n.1667G>A | non_coding_transcript_exon_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5Z1 | ENST00000649063.2 | c.1536G>A | p.Pro512= | synonymous_variant | 12/17 | NM_014855.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000724 AC: 14AN: 193452Hom.: 0 AF XY: 0.0000572 AC XY: 6AN XY: 104836
GnomAD4 exome AF: 0.0000533 AC: 76AN: 1427036Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 37AN XY: 706844
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74282
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 48 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at