6-5261420-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000324331.10(FARS2):c.-22+62G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00891 in 152,366 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 26 hom., cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FARS2
ENST00000324331.10 intron
ENST00000324331.10 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.289
Genes affected
FARS2 (HGNC:21062): (phenylalanyl-tRNA synthetase 2, mitochondrial) This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein translation. Mutations in this gene can cause combined oxidative phosphorylation deficiency 14 (Alpers encephalopathy). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 6-5261420-G-C is Benign according to our data. Variant chr6-5261420-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1190549.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00891 (1358/152366) while in subpopulation AFR AF= 0.0295 (1227/41578). AF 95% confidence interval is 0.0281. There are 26 homozygotes in gnomad4. There are 655 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_001318872.2 | c.-22+62G>C | intron_variant | ||||
FARS2 | NM_001374878.1 | c.-22+29G>C | intron_variant | ||||
FARS2 | XM_047418086.1 | c.-22+11467G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000324331.10 | c.-22+62G>C | intron_variant | 1 | P1 | ||||
FARS2 | ENST00000602691.1 | c.-326G>C | 5_prime_UTR_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00881 AC: 1341AN: 152248Hom.: 24 Cov.: 34
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 998Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 708
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GnomAD4 genome ? AF: 0.00891 AC: 1358AN: 152366Hom.: 26 Cov.: 34 AF XY: 0.00879 AC XY: 655AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 13, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at