rs367799134
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM1BP4_ModerateBP6BS2
The NM_000033.4(ABCD1):c.392G>T(p.Gly131Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000413 in 1,209,243 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000033.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.392G>T | p.Gly131Val | missense_variant | 1/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.392G>T | p.Gly131Val | missense_variant | 1/11 | ||
ABCD1 | XM_047441917.1 | c.392G>T | p.Gly131Val | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.392G>T | p.Gly131Val | missense_variant | 1/10 | 1 | NM_000033.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000530 AC: 6AN: 113308Hom.: 0 Cov.: 26 AF XY: 0.0000282 AC XY: 1AN XY: 35442
GnomAD3 exomes AF: 0.0000797 AC: 14AN: 175576Hom.: 0 AF XY: 0.0000954 AC XY: 6AN XY: 62862
GnomAD4 exome AF: 0.0000401 AC: 44AN: 1095935Hom.: 0 Cov.: 32 AF XY: 0.0000442 AC XY: 16AN XY: 362087
GnomAD4 genome AF: 0.0000530 AC: 6AN: 113308Hom.: 0 Cov.: 26 AF XY: 0.0000282 AC XY: 1AN XY: 35442
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 25, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 08, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at