chr10-112375255-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_203379.2(ACSL5):c.-30+986C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,864 control chromosomes in the GnomAD database, including 4,110 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 0.23 ( 4110 hom., cov: 31)
Exomes 𝑓: 0.16 ( 0 hom. )
Consequence
ACSL5
NM_203379.2 intron
NM_203379.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.470
Genes affected
ACSL5 (HGNC:16526): (acyl-CoA synthetase long chain family member 5) The protein encoded by this gene is an isozyme of the 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 is highly expressed in uterus and spleen, and in trace amounts in normal brain, but has markedly increased levels in malignant gliomas. This gene functions in mediating fatty acid-induced glioma cell growth. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACSL5 | NM_203379.2 | c.-30+986C>T | intron_variant | ENST00000354655.9 | NP_976313.1 | |||
ACSL5 | NM_203380.2 | c.-317C>T | upstream_gene_variant | NP_976314.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ACSL5 | ENST00000354655.9 | c.-30+986C>T | intron_variant | 2 | NM_203379.2 | ENSP00000346680.4 | ||||
ACSL5 | ENST00000393081 | c.-317C>T | 5_prime_UTR_premature_start_codon_gain_variant | 1/21 | 5 | ENSP00000376796.1 | ||||
ACSL5 | ENST00000393081 | c.-317C>T | 5_prime_UTR_variant | 1/21 | 5 | ENSP00000376796.1 |
Frequencies
GnomAD3 genomes AF: 0.231 AC: 35107AN: 151690Hom.: 4110 Cov.: 31
GnomAD3 genomes
AF:
AC:
35107
AN:
151690
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.161 AC: 9AN: 56Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 6AN XY: 36
GnomAD4 exome
AF:
AC:
9
AN:
56
Hom.:
Cov.:
0
AF XY:
AC XY:
6
AN XY:
36
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.231 AC: 35123AN: 151808Hom.: 4110 Cov.: 31 AF XY: 0.231 AC XY: 17119AN XY: 74160
GnomAD4 genome
AF:
AC:
35123
AN:
151808
Hom.:
Cov.:
31
AF XY:
AC XY:
17119
AN XY:
74160
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
673
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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