chr10-116871165-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001242699.2(ENO4):c.1088C>T(p.Thr363Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000968 in 1,550,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001242699.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENO4 | NM_001242699.2 | c.1088C>T | p.Thr363Ile | missense_variant | 9/14 | ENST00000341276.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENO4 | ENST00000341276.11 | c.1088C>T | p.Thr363Ile | missense_variant | 9/14 | 5 | NM_001242699.2 | P1 | |
ENO4 | ENST00000409522.5 | c.263C>T | p.Thr88Ile | missense_variant | 3/7 | 1 | |||
ENO4 | ENST00000369207.3 | c.560C>T | p.Thr187Ile | missense_variant | 6/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000134 AC: 2AN: 149106Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80310
GnomAD4 exome AF: 0.00000858 AC: 12AN: 1398200Hom.: 0 Cov.: 30 AF XY: 0.00000580 AC XY: 4AN XY: 689624
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.1088C>T (p.T363I) alteration is located in exon 9 (coding exon 9) of the ENO4 gene. This alteration results from a C to T substitution at nucleotide position 1088, causing the threonine (T) at amino acid position 363 to be replaced by an isoleucine (I). 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