rs431905490
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001444.3(FABP5):āc.331T>Cā(p.Leu111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000478 in 1,609,834 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.000051 ( 1 hom. )
Consequence
FABP5
NM_001444.3 synonymous
NM_001444.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.63
Genes affected
FABP5 (HGNC:3560): (fatty acid binding protein 5) This gene encodes the fatty acid binding protein found in epidermal cells, and was first identified as being upregulated in psoriasis tissue. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. FABPs may play roles in fatty acid uptake, transport, and metabolism. Polymorphisms in this gene are associated with type 2 diabetes. The human genome contains many pseudogenes similar to this locus.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP7
?
Synonymous conserved (PhyloP=-4.63 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FABP5 | NM_001444.3 | c.331T>C | p.Leu111= | synonymous_variant | 3/4 | ENST00000297258.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FABP5 | ENST00000297258.11 | c.331T>C | p.Leu111= | synonymous_variant | 3/4 | 1 | NM_001444.3 | P1 | |
FABP5 | ENST00000396359.1 | c.229T>C | p.Leu77= | synonymous_variant | 3/4 | 5 | |||
FABP5 | ENST00000481695.1 | n.292T>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
FABP5 | ENST00000486269.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152040Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000690 AC: 17AN: 246492Hom.: 1 AF XY: 0.0000825 AC XY: 11AN XY: 133356
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GnomAD4 exome AF: 0.0000508 AC: 74AN: 1457794Hom.: 1 Cov.: 30 AF XY: 0.0000607 AC XY: 44AN XY: 725176
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74252
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | literature only | Laboratory for Molecular Psychiatry, RIKEN | - | - - |
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