X-153736100-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000033.4(ABCD1):c.1082-12G>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 Uncertain significance (★).
Frequency
Consequence
NM_000033.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1082-12G>A | intron_variant | Intron 2 of 9 | ENST00000218104.6 | NP_000024.2 | ||
ABCD1 | XM_047441916.1 | c.1082-12G>A | intron_variant | Intron 2 of 10 | XP_047297872.1 | |||
ABCD1 | XM_047441917.1 | c.1082-12G>A | intron_variant | Intron 2 of 7 | XP_047297873.1 | |||
LOC124905226 | XR_007068350.1 | n.4251C>T | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1082-12G>A | intron_variant | Intron 2 of 9 | 1 | NM_000033.4 | ENSP00000218104.3 | |||
PLXNB3-AS1 | ENST00000434284.1 | n.581-141C>T | intron_variant | Intron 2 of 2 | 3 | |||||
ABCD1 | ENST00000443684.2 | n.85-12G>A | intron_variant | Intron 1 of 5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Uncertain:1
This sequence change falls in intron 2 of the ABCD1 gene. It does not directly change the encoded amino acid sequence of the ABCD1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of X-linked adrenoleukodystrophy (Invitae). ClinVar contains an entry for this variant (Variation ID: 1354588). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.