chrX-153736079-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_000033.4(ABCD1):c.1082-33C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 24)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control
Consequence
ABCD1
NM_000033.4 intron
NM_000033.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.95
Publications
0 publications found
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 was made for transcript
Our verdict: Uncertain_significance. The variant received 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
Variant X-153736079-C-A is Pathogenic according to our data. Variant chrX-153736079-C-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 811278.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000033.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
24
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1086368Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 354096
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1086368
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
354096
African (AFR)
AF:
AC:
0
AN:
26159
American (AMR)
AF:
AC:
0
AN:
35056
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19253
East Asian (EAS)
AF:
AC:
0
AN:
30027
South Asian (SAS)
AF:
AC:
0
AN:
53767
European-Finnish (FIN)
AF:
AC:
0
AN:
39202
Middle Eastern (MID)
AF:
AC:
0
AN:
3509
European-Non Finnish (NFE)
AF:
AC:
0
AN:
833821
Other (OTH)
AF:
AC:
0
AN:
45574
GnomAD4 genome
GnomAD4 genome
Cov.:
24
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Conflicting classifications of pathogenicity
Revision:criteria provided, conflicting classifications
Pathogenic
VUS
Benign
Condition
1
-
-
Adrenoleukodystrophy (1)
-
1
-
not specified (1)
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
DS_AG_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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