rs3790549
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015836.4(WARS2):āc.799G>Cā(p.Ala267Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0494 in 1,614,182 control chromosomes in the GnomAD database, including 2,726 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_015836.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WARS2 | NM_015836.4 | c.799G>C | p.Ala267Pro | missense_variant | 6/6 | ENST00000235521.5 | NP_056651.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WARS2 | ENST00000235521.5 | c.799G>C | p.Ala267Pro | missense_variant | 6/6 | 1 | NM_015836.4 | ENSP00000235521.4 | ||
WARS2 | ENST00000369426 | c.*165G>C | 3_prime_UTR_variant | 6/6 | 1 | ENSP00000358434.5 |
Frequencies
GnomAD3 genomes AF: 0.0661 AC: 10054AN: 152212Hom.: 447 Cov.: 33
GnomAD3 exomes AF: 0.0571 AC: 14338AN: 250910Hom.: 652 AF XY: 0.0554 AC XY: 7514AN XY: 135684
GnomAD4 exome AF: 0.0477 AC: 69684AN: 1461852Hom.: 2273 Cov.: 31 AF XY: 0.0478 AC XY: 34766AN XY: 727232
GnomAD4 genome AF: 0.0661 AC: 10072AN: 152330Hom.: 453 Cov.: 33 AF XY: 0.0649 AC XY: 4831AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at