chr7-4791340-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014855.3(AP5Z1):c.2379G>T(p.Thr793=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 1,609,480 control chromosomes in the GnomAD database, including 449 homozygotes. 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. T793T) has been classified as Likely benign.
Frequency
Consequence
NM_014855.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP5Z1 | NM_014855.3 | c.2379G>T | p.Thr793= | synonymous_variant | 17/17 | ENST00000649063.2 | |
AP5Z1 | NM_001364858.1 | c.1911G>T | p.Thr637= | synonymous_variant | 16/16 | ||
AP5Z1 | XM_047421098.1 | c.2043G>T | p.Thr681= | synonymous_variant | 15/15 | ||
AP5Z1 | NR_157345.1 | n.2510G>T | non_coding_transcript_exon_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP5Z1 | ENST00000649063.2 | c.2379G>T | p.Thr793= | synonymous_variant | 17/17 | NM_014855.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0160 AC: 2442AN: 152252Hom.: 32 Cov.: 33
GnomAD3 exomes AF: 0.0176 AC: 4178AN: 237522Hom.: 51 AF XY: 0.0182 AC XY: 2366AN XY: 129894
GnomAD4 exome AF: 0.0214 AC: 31118AN: 1457110Hom.: 416 Cov.: 32 AF XY: 0.0217 AC XY: 15690AN XY: 724538
GnomAD4 genome AF: 0.0160 AC: 2442AN: 152370Hom.: 33 Cov.: 33 AF XY: 0.0155 AC XY: 1157AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 23, 2019 | - - |
Hereditary spastic paraplegia 48 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Hereditary spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 09, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at