chrX-153740082-GC-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000033.4(ABCD1):c.1489-6delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00288 in 1,208,022 control chromosomes in the GnomAD database, including 103 homozygotes. There are 1,085 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000033.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1489-6delC | splice_region_variant, intron_variant | Intron 5 of 9 | ENST00000218104.6 | NP_000024.2 | ||
ABCD1 | XM_047441916.1 | c.1789-6delC | splice_region_variant, intron_variant | Intron 6 of 10 | XP_047297872.1 | |||
ABCD1 | XM_047441917.1 | c.1545-6delC | splice_region_variant, intron_variant | Intron 6 of 7 | XP_047297873.1 | |||
LOC124905226 | XR_007068350.1 | n.1465delG | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1489-9delC | intron_variant | Intron 5 of 9 | 1 | NM_000033.4 | ENSP00000218104.3 | |||
PLXNB3-AS1 | ENST00000434284.1 | n.72-1505delG | intron_variant | Intron 1 of 2 | 3 | |||||
ABCD1 | ENST00000443684.2 | n.492-9delC | intron_variant | Intron 4 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00321 AC: 362AN: 112875Hom.: 13 Cov.: 24 AF XY: 0.00337 AC XY: 118AN XY: 35023
GnomAD3 exomes AF: 0.00753 AC: 1360AN: 180604Hom.: 40 AF XY: 0.00678 AC XY: 444AN XY: 65478
GnomAD4 exome AF: 0.00284 AC: 3115AN: 1095093Hom.: 90 Cov.: 31 AF XY: 0.00268 AC XY: 966AN XY: 360949
GnomAD4 genome AF: 0.00320 AC: 361AN: 112929Hom.: 13 Cov.: 24 AF XY: 0.00339 AC XY: 119AN XY: 35087
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:6
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not provided Benign:4
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This variant is associated with the following publications: (PMID: 14556192, 24788897, 16996397, 22995991, 23835273) -
not specified Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at