chr5-168486508-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002887.4(RARS1):c.10C>T(p.Leu4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000727 in 1,559,062 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. L4L) has been classified as Likely benign.
Frequency
Consequence
NM_002887.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RARS1 | NM_002887.4 | c.10C>T | p.Leu4= | synonymous_variant | 1/15 | ENST00000231572.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RARS1 | ENST00000231572.8 | c.10C>T | p.Leu4= | synonymous_variant | 1/15 | 1 | NM_002887.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00139 AC: 211AN: 152182Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00131 AC: 218AN: 166496Hom.: 1 AF XY: 0.00134 AC XY: 118AN XY: 87850
GnomAD4 exome AF: 0.000656 AC: 923AN: 1406762Hom.: 4 Cov.: 35 AF XY: 0.000657 AC XY: 456AN XY: 694354
GnomAD4 genome ? AF: 0.00139 AC: 211AN: 152300Hom.: 2 Cov.: 32 AF XY: 0.00191 AC XY: 142AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at