chr14-102452512-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_014844.5(TECPR2):c.3525C>T(p.Ala1175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,612,760 control chromosomes in the GnomAD database, including 1 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. A1175A) has been classified as Likely benign.
Frequency
Consequence
NM_014844.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.3525C>T | p.Ala1175= | synonymous_variant | 16/20 | ENST00000359520.12 | |
TECPR2 | NM_001172631.3 | c.3525C>T | p.Ala1175= | synonymous_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.3525C>T | p.Ala1175= | synonymous_variant | 16/20 | 1 | NM_014844.5 | P1 | |
TECPR2 | ENST00000558678.1 | c.3525C>T | p.Ala1175= | synonymous_variant | 16/17 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000448 AC: 11AN: 245432Hom.: 0 AF XY: 0.0000598 AC XY: 8AN XY: 133694
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460400Hom.: 1 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 726526
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152360Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | TECPR2: BP4, BP7 - |
Hereditary spastic paraplegia 49 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at