14-100337161-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004184.4(WARS1):c.1155G>T(p.Glu385Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,046 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WARS1 | NM_004184.4 | c.1155G>T | p.Glu385Asp | missense_variant | Exon 10 of 11 | ENST00000392882.7 | NP_004175.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251490Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461840Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727226
GnomAD4 genome AF: 0.000125 AC: 19AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1155G>T (p.E385D) alteration is located in exon 10 (coding exon 9) of the WARS gene. This alteration results from a G to T substitution at nucleotide position 1155, causing the glutamic acid (E) at amino acid position 385 to be replaced by an aspartic acid (D). 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