chr2-222571940-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_005687.5(FARSB):c.1701C>T(p.Asp567=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,613,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
FARSB
NM_005687.5 synonymous
NM_005687.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.834
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 -15 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 2-222571940-G-A is Benign according to our data. Variant chr2-222571940-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1581206.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.834 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00015 (219/1461586) while in subpopulation NFE AF= 0.000192 (214/1111798). AF 95% confidence interval is 0.000171. There are 0 homozygotes in gnomad4_exome. There are 116 alleles in male gnomad4_exome subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARSB | NM_005687.5 | c.1701C>T | p.Asp567= | synonymous_variant | 17/17 | ENST00000281828.8 | |
FARSB | XM_006712169.3 | c.1404C>T | p.Asp468= | synonymous_variant | 18/18 | ||
FARSB | XM_011510466.3 | c.1404C>T | p.Asp468= | synonymous_variant | 18/18 | ||
FARSB | NR_130154.2 | n.1916C>T | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARSB | ENST00000281828.8 | c.1701C>T | p.Asp567= | synonymous_variant | 17/17 | 1 | NM_005687.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000987 AC: 15AN: 152020Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251132Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135720
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GnomAD4 exome AF: 0.000150 AC: 219AN: 1461586Hom.: 0 Cov.: 33 AF XY: 0.000160 AC XY: 116AN XY: 727116
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2023 | - - |
FARSB-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at