chr14-102445813-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014844.5(TECPR2):c.2941C>A(p.Gln981Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,613,582 control chromosomes in the GnomAD database, including 361 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.2941C>A | p.Gln981Lys | missense_variant | Exon 13 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | ||
TECPR2 | ENST00000558678.1 | c.2941C>A | p.Gln981Lys | missense_variant | Exon 13 of 17 | 1 | ENSP00000453671.1 | |||
TECPR2 | ENST00000557786.1 | n.550C>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0142 AC: 2158AN: 151958Hom.: 24 Cov.: 31
GnomAD3 exomes AF: 0.0172 AC: 4327AN: 251142Hom.: 49 AF XY: 0.0184 AC XY: 2504AN XY: 135766
GnomAD4 exome AF: 0.0199 AC: 29031AN: 1461506Hom.: 337 Cov.: 31 AF XY: 0.0200 AC XY: 14566AN XY: 727064
GnomAD4 genome AF: 0.0142 AC: 2159AN: 152076Hom.: 24 Cov.: 31 AF XY: 0.0138 AC XY: 1027AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
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Hereditary spastic paraplegia 49 Benign:2
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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