3-49101373-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005051.3(QARS1):c.858C>A(p.Phe286Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,402 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005051.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
QARS1 | NM_005051.3 | c.858C>A | p.Phe286Leu | missense_variant | Exon 10 of 24 | ENST00000306125.12 | NP_005042.1 | |
QARS1 | NM_001272073.2 | c.825C>A | p.Phe275Leu | missense_variant | Exon 10 of 24 | NP_001259002.1 | ||
QARS1 | XM_017006965.3 | c.858C>A | p.Phe286Leu | missense_variant | Exon 10 of 23 | XP_016862454.2 | ||
QARS1 | NR_073590.2 | n.833C>A | non_coding_transcript_exon_variant | Exon 10 of 24 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461402Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727024
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:3
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Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 25471517) -
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Inborn genetic diseases Uncertain:1
The c.858C>A (p.F286L) alteration is located in exon 10 (coding exon 10) of the QARS gene. This alteration results from a C to A substitution at nucleotide position 858, causing the phenylalanine (F) at amino acid position 286 to be replaced by a leucine (L). 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