7-4789918-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_014855.3(AP5Z1):āc.1794C>Gā(p.Ala598=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,545,680 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. A598A) has been classified as Likely benign.
Frequency
Consequence
NM_014855.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP5Z1 | NM_014855.3 | c.1794C>G | p.Ala598= | synonymous_variant | 14/17 | ENST00000649063.2 | |
AP5Z1 | NM_001364858.1 | c.1326C>G | p.Ala442= | synonymous_variant | 13/16 | ||
AP5Z1 | XM_047421098.1 | c.1458C>G | p.Ala486= | synonymous_variant | 12/15 | ||
AP5Z1 | NR_157345.1 | n.1925C>G | non_coding_transcript_exon_variant | 14/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5Z1 | ENST00000649063.2 | c.1794C>G | p.Ala598= | synonymous_variant | 14/17 | NM_014855.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000535 AC: 8AN: 149412Hom.: 0 AF XY: 0.0000377 AC XY: 3AN XY: 79648
GnomAD4 exome AF: 0.000199 AC: 278AN: 1393610Hom.: 0 Cov.: 32 AF XY: 0.000207 AC XY: 142AN XY: 686910
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74264
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 48 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at