rs729662
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001014437.3(CARS1):c.2118C>T(p.Pro706=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,613,298 control chromosomes in the GnomAD database, including 81,250 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 6752 hom., cov: 34)
Exomes 𝑓: 0.31 ( 74498 hom. )
Consequence
CARS1
NM_001014437.3 synonymous
NM_001014437.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.85
Genes affected
CARS1 (HGNC:1493): (cysteinyl-tRNA synthetase 1) This gene encodes a class 1 aminoacyl-tRNA synthetase, cysteinyl-tRNA synthetase. Each of the twenty aminoacyl-tRNA synthetases catalyzes the aminoacylation of a specific tRNA or tRNA isoaccepting family with the cognate amino acid. This gene is one of several located near the imprinted gene domain on chromosome 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian and breast cancers. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP7
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Synonymous conserved (PhyloP=-1.85 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARS1 | NM_001014437.3 | c.2118C>T | p.Pro706= | synonymous_variant | 19/23 | ENST00000380525.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARS1 | ENST00000380525.9 | c.2118C>T | p.Pro706= | synonymous_variant | 19/23 | 1 | NM_001014437.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.260 AC: 39490AN: 152140Hom.: 6740 Cov.: 34
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GnomAD3 exomes AF: 0.350 AC: 87746AN: 251038Hom.: 18152 AF XY: 0.346 AC XY: 46973AN XY: 135716
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GnomAD4 exome AF: 0.305 AC: 446304AN: 1461040Hom.: 74498 Cov.: 35 AF XY: 0.307 AC XY: 223333AN XY: 726846
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GnomAD4 genome ? AF: 0.260 AC: 39511AN: 152258Hom.: 6752 Cov.: 34 AF XY: 0.264 AC XY: 19624AN XY: 74452
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at