rs12523547
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001445.3(FABP6):c.333+808G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,988 control chromosomes in the GnomAD database, including 15,232 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.44 ( 15232 hom., cov: 32)
Consequence
FABP6
NM_001445.3 intron
NM_001445.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0340
Genes affected
FABP6 (HGNC:3561): (fatty acid binding protein 6) This gene encodes the ileal fatty acid binding protein. Fatty acid binding proteins are a family of small, highly conserved, cytoplasmic proteins that bind long-chain fatty acids and other hydrophobic ligands. FABP6 and FABP1 (the liver fatty acid binding protein) are also able to bind bile acids. It is thought that FABPs roles include fatty acid uptake, transport, and metabolism. Transcript variants generated by alternate transcription promoters and/or alternate splicing have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FABP6 | NM_001445.3 | c.333+808G>C | intron_variant | ENST00000402432.4 | |||
FABP6 | NM_001040442.1 | c.480+808G>C | intron_variant | ||||
FABP6 | NM_001130958.2 | c.480+808G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FABP6 | ENST00000402432.4 | c.333+808G>C | intron_variant | 1 | NM_001445.3 | P1 | |||
FABP6 | ENST00000393980.8 | c.480+808G>C | intron_variant | 1 | |||||
FABP6 | ENST00000523955.5 | c.*541+808G>C | intron_variant, NMD_transcript_variant | 3 | |||||
FABP6 | ENST00000521362.1 | n.329+808G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.444 AC: 67451AN: 151870Hom.: 15220 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.444 AC: 67500AN: 151988Hom.: 15232 Cov.: 32 AF XY: 0.450 AC XY: 33413AN XY: 74282
GnomAD4 genome
?
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67500
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32
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33413
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74282
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1876
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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