X-153743457-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000033.4(ABCD1):c.1992-32C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.59 ( 13955 hom., 19421 hem., cov: 22)
Exomes 𝑓: 0.64 ( 147059 hom. 227195 hem. )
Failed GnomAD Quality Control
Consequence
ABCD1
NM_000033.4 intron
NM_000033.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.08
Genes affected
ABCD1 (HGNC:61): (ATP binding cassette subfamily D member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ALD subfamily, which is involved in peroxisomal import of fatty acids and/or fatty acyl-CoAs in the organelle. All known peroxisomal ABC transporters are half transporters which require a partner half transporter molecule to form a functional homodimeric or heterodimeric transporter. This peroxisomal membrane protein is likely involved in the peroxisomal transport or catabolism of very long chain fatty acids. Defects in this gene have been identified as the underlying cause of adrenoleukodystrophy, an X-chromosome recessively inherited demyelinating disorder of the nervous system. [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=-0.86).
BP6
Variant X-153743457-C-T is Benign according to our data. Variant chrX-153743457-C-T is described in ClinVar as [Benign]. Clinvar id is 439347.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1992-32C>T | intron_variant | ENST00000218104.6 | NP_000024.2 | |||
ABCD1 | XM_047441916.1 | c.2292-32C>T | intron_variant | XP_047297872.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1992-32C>T | intron_variant | 1 | NM_000033.4 | ENSP00000218104.3 | ||||
PLXNB3-AS1 | ENST00000434284.1 | n.72-4879G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.594 AC: 65532AN: 110381Hom.: 13954 Cov.: 22 AF XY: 0.593 AC XY: 19381AN XY: 32657
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GnomAD3 exomes AF: 0.628 AC: 97817AN: 155788Hom.: 21314 AF XY: 0.629 AC XY: 30750AN XY: 48858
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.636 AC: 689259AN: 1083863Hom.: 147059 Cov.: 41 AF XY: 0.642 AC XY: 227195AN XY: 354053
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.594 AC: 65567AN: 110435Hom.: 13955 Cov.: 22 AF XY: 0.594 AC XY: 19421AN XY: 32721
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 02, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 06, 2019 | - - |
Adrenoleukodystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
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