chr12-29332635-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001271783.2(FAR2):c.1293G>A(p.Leu431=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000268 in 1,613,662 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00015 ( 2 hom. )
Consequence
FAR2
NM_001271783.2 synonymous
NM_001271783.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.615
Genes affected
FAR2 (HGNC:25531): (fatty acyl-CoA reductase 2) This gene belongs to the short chain dehydrogenase/reductase superfamily. It encodes a reductase enzyme involved in the first step of wax biosynthesis wherein fatty acids are converted to fatty alcohols. The encoded peroxisomal protein utilizes saturated fatty acids of 16 or 18 carbons as preferred substrates. Alternatively spliced transcript variants have been observed for this gene. Related pseudogenes have been identified on chromosomes 2, 14 and 22. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 12-29332635-G-A is Benign according to our data. Variant chr12-29332635-G-A is described in ClinVar as [Benign]. Clinvar id is 744520.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.615 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAR2 | NM_001271783.2 | c.1293G>A | p.Leu431= | synonymous_variant | 11/12 | ENST00000536681.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAR2 | ENST00000536681.8 | c.1293G>A | p.Leu431= | synonymous_variant | 11/12 | 1 | NM_001271783.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00143 AC: 218AN: 152062Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000418 AC: 105AN: 251198Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135756
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GnomAD4 exome AF: 0.000146 AC: 213AN: 1461482Hom.: 2 Cov.: 32 AF XY: 0.000110 AC XY: 80AN XY: 727038
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GnomAD4 genome ? AF: 0.00144 AC: 219AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00152 AC XY: 113AN XY: 74396
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 15, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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