chr1-94418486-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002858.4(ABCD3):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,600,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Likely benign.
Frequency
Consequence
NM_002858.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD3 | NM_002858.4 | c.8C>T | p.Ala3Val | missense_variant | 1/23 | ENST00000370214.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD3 | ENST00000370214.9 | c.8C>T | p.Ala3Val | missense_variant | 1/23 | 1 | NM_002858.4 | P3 | |
ABCD3 | ENST00000315713.5 | c.8C>T | p.Ala3Val | missense_variant | 1/9 | 1 | |||
ABCD3 | ENST00000647998.2 | c.8C>T | p.Ala3Val | missense_variant | 1/23 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000654 AC: 15AN: 229372Hom.: 0 AF XY: 0.0000396 AC XY: 5AN XY: 126280
GnomAD4 exome AF: 0.000122 AC: 176AN: 1448448Hom.: 0 Cov.: 31 AF XY: 0.000103 AC XY: 74AN XY: 720738
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.8C>T (p.A3V) alteration is located in exon 1 (coding exon 1) of the ABCD3 gene. This alteration results from a C to T substitution at nucleotide position 8, causing the alanine (A) at amino acid position 3 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3 of the ABCD3 protein (p.Ala3Val). This variant is present in population databases (rs150616788, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ABCD3-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at