10-116881628-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242699.2(ENO4):c.1837G>C(p.Gly613Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,549,564 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/18 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENO4 | NM_001242699.2 | c.1837G>C | p.Gly613Arg | missense_variant | 14/14 | ENST00000341276.11 | |
SHTN1 | NM_001127211.3 | c.*4716C>G | 3_prime_UTR_variant | 17/17 | ENST00000355371.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENO4 | ENST00000341276.11 | c.1837G>C | p.Gly613Arg | missense_variant | 14/14 | 5 | NM_001242699.2 | P1 | |
SHTN1 | ENST00000355371.9 | c.*4716C>G | 3_prime_UTR_variant | 17/17 | 2 | NM_001127211.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000808 AC: 12AN: 148484Hom.: 0 AF XY: 0.0000875 AC XY: 7AN XY: 79986
GnomAD4 exome AF: 0.0000122 AC: 17AN: 1397376Hom.: 0 Cov.: 30 AF XY: 0.0000116 AC XY: 8AN XY: 689080
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1837G>C (p.G613R) alteration is located in exon 14 (coding exon 14) of the ENO4 gene. This alteration results from a G to C substitution at nucleotide position 1837, causing the glycine (G) at amino acid position 613 to be replaced by an arginine (R). 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