rs144147210
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_014844.5(TECPR2):āc.2939G>Cā(p.Arg980Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00248 in 1,613,744 control chromosomes in the GnomAD database, including 19 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 Likely benign (ā ā ).
Frequency
Consequence
NM_014844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.2939G>C | p.Arg980Thr | missense_variant | 13/20 | ENST00000359520.12 | |
TECPR2 | NM_001172631.3 | c.2939G>C | p.Arg980Thr | missense_variant | 13/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.2939G>C | p.Arg980Thr | missense_variant | 13/20 | 1 | NM_014844.5 | P1 | |
TECPR2 | ENST00000558678.1 | c.2939G>C | p.Arg980Thr | missense_variant | 13/17 | 1 | |||
TECPR2 | ENST00000557786.1 | n.548G>C | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00310 AC: 471AN: 152010Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00348 AC: 874AN: 251172Hom.: 6 AF XY: 0.00345 AC XY: 469AN XY: 135772
GnomAD4 exome AF: 0.00241 AC: 3526AN: 1461616Hom.: 16 Cov.: 30 AF XY: 0.00236 AC XY: 1717AN XY: 727104
GnomAD4 genome ? AF: 0.00310 AC: 471AN: 152128Hom.: 3 Cov.: 31 AF XY: 0.00411 AC XY: 306AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | TECPR2: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 16, 2019 | - - |
Hereditary spastic paraplegia 49 Benign:2
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hereditary spastic paraplegia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at