X-153743269-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_000033.4(ABCD1):c.1914C>T(p.Asp638=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000978 in 1,206,150 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 41 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000033.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1914C>T | p.Asp638= | synonymous_variant | 9/10 | ENST00000218104.6 | NP_000024.2 | |
ABCD1 | XM_047441916.1 | c.2214C>T | p.Asp738= | synonymous_variant | 10/11 | XP_047297872.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1914C>T | p.Asp638= | synonymous_variant | 9/10 | 1 | NM_000033.4 | ENSP00000218104 | P1 | |
PLXNB3-AS1 | ENST00000434284.1 | n.72-4691G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000621 AC: 7AN: 112749Hom.: 0 Cov.: 24 AF XY: 0.0000573 AC XY: 2AN XY: 34905
GnomAD3 exomes AF: 0.0000638 AC: 11AN: 172412Hom.: 0 AF XY: 0.0000507 AC XY: 3AN XY: 59148
GnomAD4 exome AF: 0.000102 AC: 111AN: 1093401Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 39AN XY: 360159
GnomAD4 genome AF: 0.0000621 AC: 7AN: 112749Hom.: 0 Cov.: 24 AF XY: 0.0000573 AC XY: 2AN XY: 34905
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 16, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ABCD1: BP4, BP7 - |
ABCD1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 03, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at