rs75004775
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014844.5(TECPR2):c.3465C>A(p.Ser1155Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000744 in 1,613,698 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1155S) has been classified as Likely benign.
Frequency
Consequence
NM_014844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.3465C>A | p.Ser1155Arg | missense_variant | 16/20 | ENST00000359520.12 | |
TECPR2 | NM_001172631.3 | c.3465C>A | p.Ser1155Arg | missense_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.3465C>A | p.Ser1155Arg | missense_variant | 16/20 | 1 | NM_014844.5 | P1 | |
TECPR2 | ENST00000558678.1 | c.3465C>A | p.Ser1155Arg | missense_variant | 16/17 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000749 AC: 114AN: 152276Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00158 AC: 391AN: 248182Hom.: 7 AF XY: 0.00159 AC XY: 214AN XY: 134604
GnomAD4 exome AF: 0.000744 AC: 1087AN: 1461304Hom.: 14 Cov.: 33 AF XY: 0.000763 AC XY: 555AN XY: 726948
GnomAD4 genome ? AF: 0.000741 AC: 113AN: 152394Hom.: 4 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74522
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 49 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Hereditary spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 13, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at