10-116881569-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001242699.2(ENO4):c.1778C>T(p.Ala593Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,549,912 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENO4 | ENST00000341276.11 | c.1778C>T | p.Ala593Val | missense_variant | Exon 14 of 14 | 5 | NM_001242699.2 | ENSP00000345555.6 | ||
SHTN1 | ENST00000355371 | c.*4775G>A | 3_prime_UTR_variant | Exon 17 of 17 | 2 | NM_001127211.3 | ENSP00000347532.4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000336 AC: 5AN: 148792Hom.: 0 AF XY: 0.0000374 AC XY: 3AN XY: 80170
GnomAD4 exome AF: 0.0000451 AC: 63AN: 1397768Hom.: 0 Cov.: 30 AF XY: 0.0000363 AC XY: 25AN XY: 689396
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152144Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1778C>T (p.A593V) alteration is located in exon 14 (coding exon 14) of the ENO4 gene. This alteration results from a C to T substitution at nucleotide position 1778, causing the alanine (A) at amino acid position 593 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