X-153725867-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2
The NM_000033.4(ABCD1):c.601G>A(p.Val201Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,210,757 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 29 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. V201V) 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.601G>A | p.Val201Met | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.601G>A | p.Val201Met | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.601G>A | p.Val201Met | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.601G>A | p.Val201Met | missense_variant | 1/10 | 1 | NM_000033.4 | P1 | |
ABCD1 | ENST00000370129.4 | c.46G>A | p.Val16Met | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000476 AC: 54AN: 113500Hom.: 0 Cov.: 26 AF XY: 0.000253 AC XY: 9AN XY: 35636
GnomAD3 exomes AF: 0.000148 AC: 27AN: 181930Hom.: 0 AF XY: 0.000149 AC XY: 10AN XY: 66918
GnomAD4 exome AF: 0.0000702 AC: 77AN: 1097204Hom.: 0 Cov.: 32 AF XY: 0.0000551 AC XY: 20AN XY: 362994
GnomAD4 genome AF: 0.000476 AC: 54AN: 113553Hom.: 0 Cov.: 26 AF XY: 0.000252 AC XY: 9AN XY: 35699
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 05, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ABCD1: BS2 - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 28, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
ABCD1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 06, 2023 | 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