rs782327280
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2
The NM_000033.4(ABCD1):c.2043C>G(p.Phe681Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,201,576 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. F681F) has been classified as Likely benign.
Frequency
Consequence
NM_000033.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.2043C>G | p.Phe681Leu | missense_variant | 10/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.2343C>G | p.Phe781Leu | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.2043C>G | p.Phe681Leu | missense_variant | 10/10 | 1 | NM_000033.4 | P1 | |
PLXNB3-AS1 | ENST00000434284.1 | n.72-4962G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000177 AC: 2AN: 112687Hom.: 0 Cov.: 24 AF XY: 0.0000574 AC XY: 2AN XY: 34861
GnomAD3 exomes AF: 0.000159 AC: 26AN: 163919Hom.: 1 AF XY: 0.0000744 AC XY: 4AN XY: 53785
GnomAD4 exome AF: 0.0000156 AC: 17AN: 1088889Hom.: 0 Cov.: 37 AF XY: 0.0000112 AC XY: 4AN XY: 356639
GnomAD4 genome ? AF: 0.0000177 AC: 2AN: 112687Hom.: 0 Cov.: 24 AF XY: 0.0000574 AC XY: 2AN XY: 34861
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 26, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 20, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at