X-153736099-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000033.4(ABCD1):c.1082-13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000117 in 856,332 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000033.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1082-13T>C | intron_variant | Intron 2 of 9 | ENST00000218104.6 | NP_000024.2 | ||
ABCD1 | XM_047441916.1 | c.1082-13T>C | intron_variant | Intron 2 of 10 | XP_047297872.1 | |||
ABCD1 | XM_047441917.1 | c.1082-13T>C | intron_variant | Intron 2 of 7 | XP_047297873.1 | |||
LOC124905226 | XR_007068350.1 | n.4252A>G | 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.1082-13T>C | intron_variant | Intron 2 of 9 | 1 | NM_000033.4 | ENSP00000218104.3 | |||
PLXNB3-AS1 | ENST00000434284.1 | n.581-140A>G | intron_variant | Intron 2 of 2 | 3 | |||||
ABCD1 | ENST00000443684.2 | n.85-13T>C | intron_variant | Intron 1 of 5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 0.00000117 AC: 1AN: 856332Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 268276
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.