X-153737192-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP6_ModerateBS2
The NM_000033.4(ABCD1):c.1429G>A(p.Glu477Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000908 in 1,210,992 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. E477E) has been classified as Likely benign.
Frequency
Consequence
NM_000033.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1429G>A | p.Glu477Lys | missense_variant | 5/10 | ENST00000218104.6 | |
LOC124905226 | XR_007068350.1 | n.3159C>T | non_coding_transcript_exon_variant | 2/2 | |||
ABCD1 | XM_047441916.1 | c.1729G>A | p.Glu577Lys | missense_variant | 6/11 | ||
ABCD1 | XM_047441917.1 | c.1485G>A | p.Ala495= | synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1429G>A | p.Glu477Lys | missense_variant | 5/10 | 1 | NM_000033.4 | P1 | |
PLXNB3-AS1 | ENST00000434284.1 | n.580+878C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ABCD1 | ENST00000443684.2 | n.432G>A | non_coding_transcript_exon_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000265 AC: 3AN: 113365Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35505
GnomAD3 exomes AF: 0.0000220 AC: 4AN: 182081Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67225
GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097627Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 363185
GnomAD4 genome AF: 0.0000265 AC: 3AN: 113365Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35505
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at