rs1554181180
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_006567.5(FARS2):c.613-4A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,422,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006567.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.613-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000274680.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.613-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006567.5 | P1 | |||
FARS2 | ENST00000324331.10 | c.613-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
FARS2 | ENST00000648580.1 | c.613-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | ||||||
FARS2 | ENST00000445533.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1422760Hom.: 0 Cov.: 30 AF XY: 0.00000284 AC XY: 2AN XY: 704532
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at