14-102376786-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014844.5(TECPR2):c.65C>T(p.Ala22Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.65C>T | p.Ala22Val | missense_variant | Exon 2 of 20 | ENST00000359520.12 | NP_055659.2 | |
TECPR2 | NM_001172631.3 | c.65C>T | p.Ala22Val | missense_variant | Exon 2 of 17 | NP_001166102.1 | ||
LOC124903389 | XR_007064350.1 | n.73-6301G>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.65C>T | p.Ala22Val | missense_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | ||
TECPR2 | ENST00000558678.1 | c.65C>T | p.Ala22Val | missense_variant | Exon 2 of 17 | 1 | ENSP00000453671.1 | |||
TECPR2 | ENST00000561228.1 | n.193C>T | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251474Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727246
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.65C>T (p.A22V) alteration is located in exon 2 (coding exon 1) of the TECPR2 gene. This alteration results from a C to T substitution at nucleotide position 65, causing the alanine (A) at amino acid position 22 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at