X-153726023-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_000033.4(ABCD1):c.757C>T(p.Leu253Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000917 in 1,090,716 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L253V) has been classified as Likely benign.
Frequency
Consequence
NM_000033.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.757C>T | p.Leu253Phe | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.757C>T | p.Leu253Phe | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.757C>T | p.Leu253Phe | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.757C>T | p.Leu253Phe | missense_variant | 1/10 | 1 | NM_000033.4 | P1 | |
ABCD1 | ENST00000370129.4 | c.202C>T | p.Leu68Phe | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 26
GnomAD4 exome AF: 9.17e-7 AC: 1AN: 1090716Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 357752
GnomAD4 genome ? Cov.: 26
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2019 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at