chr7-98217437-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015395.3(TECPR1):āc.3451C>Gā(p.Gln1151Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,609,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015395.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECPR1 | NM_015395.3 | c.3451C>G | p.Gln1151Glu | missense_variant | 26/26 | ENST00000447648.7 | |
TECPR1 | XM_005250253.5 | c.3451C>G | p.Gln1151Glu | missense_variant | 26/26 | ||
TECPR1 | XM_017011937.2 | c.3349C>G | p.Gln1117Glu | missense_variant | 25/25 | ||
TECPR1 | XM_047420119.1 | c.3349C>G | p.Gln1117Glu | missense_variant | 25/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECPR1 | ENST00000447648.7 | c.3451C>G | p.Gln1151Glu | missense_variant | 26/26 | 1 | NM_015395.3 | P1 | |
TECPR1 | ENST00000490842.5 | n.2649C>G | non_coding_transcript_exon_variant | 15/16 | 1 | ||||
TECPR1 | ENST00000463402.5 | n.963C>G | non_coding_transcript_exon_variant | 5/5 | 2 | ||||
TECPR1 | ENST00000485716.1 | n.214C>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238870Hom.: 0 AF XY: 0.0000382 AC XY: 5AN XY: 130894
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1457032Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 724506
GnomAD4 genome AF: 0.000236 AC: 36AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.3451C>G (p.Q1151E) alteration is located in exon 26 (coding exon 24) of the TECPR1 gene. This alteration results from a C to G substitution at nucleotide position 3451, causing the glutamine (Q) at amino acid position 1151 to be replaced by a glutamic acid (E). 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