chr2-222599911-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005687.5(FARSB):c.1618+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000892 in 1,565,790 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00053 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 26 hom. )
Consequence
FARSB
NM_005687.5 intron
NM_005687.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.877
Genes affected
FARSB (HGNC:17800): (phenylalanyl-tRNA synthetase subunit beta) This gene encodes a highly conserved enzyme that belongs to the aminoacyl-tRNA synthetase class IIc subfamily. This enzyme comprises the regulatory beta subunits that form a tetramer with two catalytic alpha subunits. In the presence of ATP, this tetramer is responsible for attaching L-phenylalanine to the terminal adenosine of the appropriate tRNA. A pseudogene located on chromosome 10 has been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 2-222599911-C-T is Benign according to our data. Variant chr2-222599911-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1542704.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000532 (81/152282) while in subpopulation SAS AF= 0.016 (77/4826). AF 95% confidence interval is 0.0131. There are 1 homozygotes in gnomad4. There are 56 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARSB | NM_005687.5 | c.1618+17G>A | intron_variant | ENST00000281828.8 | |||
FARSB | XM_006712169.3 | c.1321+17G>A | intron_variant | ||||
FARSB | XM_011510466.3 | c.1321+17G>A | intron_variant | ||||
FARSB | NR_130154.2 | n.1833+17G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARSB | ENST00000281828.8 | c.1618+17G>A | intron_variant | 1 | NM_005687.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000539 AC: 82AN: 152164Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00203 AC: 425AN: 209784Hom.: 5 AF XY: 0.00273 AC XY: 313AN XY: 114638
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GnomAD4 exome AF: 0.000930 AC: 1315AN: 1413508Hom.: 26 Cov.: 29 AF XY: 0.00136 AC XY: 953AN XY: 702458
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GnomAD4 genome ? AF: 0.000532 AC: 81AN: 152282Hom.: 1 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74460
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Rajab interstitial lung disease with brain calcifications 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 28, 2021 | - - |
Computational 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
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