chr8-81283899-A-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001444.3(FABP5):c.279A>G(p.Ala93Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,458 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 not provided (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FABP5
NM_001444.3 synonymous
NM_001444.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
Publications
1 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP7
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FABP5 | ENST00000297258.11 | c.279A>G | p.Ala93Ala | synonymous_variant | Exon 3 of 4 | 1 | NM_001444.3 | ENSP00000297258.6 | ||
| FABP5 | ENST00000396359.1 | c.177A>G | p.Ala59Ala | synonymous_variant | Exon 3 of 4 | 5 | ENSP00000379647.1 | |||
| FABP5 | ENST00000481695.1 | n.240A>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
| FABP5 | ENST00000486269.1 | n.538A>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460458Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726480 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1460458
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726480
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33418
American (AMR)
AF:
AC:
0
AN:
44716
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26130
East Asian (EAS)
AF:
AC:
0
AN:
39648
South Asian (SAS)
AF:
AC:
0
AN:
86094
European-Finnish (FIN)
AF:
AC:
0
AN:
53292
Middle Eastern (MID)
AF:
AC:
0
AN:
5614
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111244
Other (OTH)
AF:
AC:
0
AN:
60302
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
-
Laboratory for Molecular Psychiatry, RIKEN
Significance:not provided
Review Status:no classification provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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