rs17415911
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003645.4(SLC27A2):c.848-142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 904,052 control chromosomes in the GnomAD database, including 11,316 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 0.12 ( 1387 hom., cov: 30)
Exomes 𝑓: 0.15 ( 9929 hom. )
Consequence
SLC27A2
NM_003645.4 intron
NM_003645.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.481
Genes affected
SLC27A2 (HGNC:10996): (solute carrier family 27 member 2) The protein encoded by this gene is an isozyme of long-chain fatty-acid-coenzyme A ligase family. Although differing in substrate specificity, subcellular localization, and tissue distribution, all isozymes of this family convert free long-chain fatty acids into fatty acyl-CoA esters, and thereby play a key role in lipid biosynthesis and fatty acid degradation. This isozyme activates long-chain, branched-chain and very-long-chain fatty acids containing 22 or more carbons to their CoA derivatives. It is expressed primarily in liver and kidney, and is present in both endoplasmic reticulum and peroxisomes, but not in mitochondria. Its decreased peroxisomal enzyme activity is in part responsible for the biochemical pathology in X-linked adrenoleukodystrophy. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]
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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=-0.62).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC27A2 | NM_003645.4 | c.848-142A>G | intron_variant | ENST00000267842.10 | |||
SLC27A2 | NM_001159629.2 | c.689-142A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC27A2 | ENST00000267842.10 | c.848-142A>G | intron_variant | 1 | NM_003645.4 | P1 | |||
SLC27A2 | ENST00000380902.8 | c.689-142A>G | intron_variant | 1 | |||||
SLC27A2 | ENST00000544960.1 | c.143-142A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.121 AC: 18416AN: 151852Hom.: 1387 Cov.: 30
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GnomAD4 exome AF: 0.155 AC: 116201AN: 752086Hom.: 9929 AF XY: 0.154 AC XY: 57921AN XY: 375584
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GnomAD4 genome ? AF: 0.121 AC: 18415AN: 151966Hom.: 1387 Cov.: 30 AF XY: 0.117 AC XY: 8721AN XY: 74282
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at