chr3-49103687-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_005051.3(QARS1):āc.395G>Cā(p.Arg132Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,613,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005051.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
QARS1 | NM_005051.3 | c.395G>C | p.Arg132Thr | missense_variant | Exon 4 of 24 | ENST00000306125.12 | NP_005042.1 | |
QARS1 | NM_001272073.2 | c.362G>C | p.Arg121Thr | missense_variant | Exon 4 of 24 | NP_001259002.1 | ||
QARS1 | XM_017006965.3 | c.395G>C | p.Arg132Thr | missense_variant | Exon 4 of 23 | XP_016862454.2 | ||
QARS1 | NR_073590.2 | n.370G>C | non_coding_transcript_exon_variant | Exon 4 of 24 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000760 AC: 190AN: 250092Hom.: 0 AF XY: 0.000466 AC XY: 63AN XY: 135282
GnomAD4 exome AF: 0.000138 AC: 201AN: 1461454Hom.: 0 Cov.: 31 AF XY: 0.0000963 AC XY: 70AN XY: 726992
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
Diffuse cerebral and cerebellar atrophy - intractable seizures - progressive microcephaly syndrome Benign:2
BS1, BP4 -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at