NM_014844.5:c.-2C>T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_014844.5(TECPR2):c.-2C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0333 in 1,613,746 control chromosomes in the GnomAD database, including 1,257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014844.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.-2C>T | 5_prime_UTR_variant | Exon 2 of 20 | ENST00000359520.12 | NP_055659.2 | ||
TECPR2 | NM_001172631.3 | c.-2C>T | 5_prime_UTR_variant | Exon 2 of 17 | NP_001166102.1 | |||
LOC124903389 | XR_007064350.1 | n.73-6235G>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520 | c.-2C>T | 5_prime_UTR_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | |||
TECPR2 | ENST00000558678 | c.-2C>T | 5_prime_UTR_variant | Exon 2 of 17 | 1 | ENSP00000453671.1 | ||||
TECPR2 | ENST00000561228.1 | n.127C>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0264 AC: 4014AN: 152192Hom.: 88 Cov.: 32
GnomAD3 exomes AF: 0.0343 AC: 8609AN: 251314Hom.: 292 AF XY: 0.0393 AC XY: 5344AN XY: 135828
GnomAD4 exome AF: 0.0340 AC: 49761AN: 1461436Hom.: 1169 Cov.: 31 AF XY: 0.0364 AC XY: 26486AN XY: 727032
GnomAD4 genome AF: 0.0264 AC: 4014AN: 152310Hom.: 88 Cov.: 32 AF XY: 0.0274 AC XY: 2037AN XY: 74476
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 49 Benign:2
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not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Hereditary spastic paraplegia Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at