rs193922096
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000033.4(ABCD1):c.2190G>A(p.Pro730=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,170,183 control chromosomes in the GnomAD database, including 2 homozygotes. There are 468 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. P730P) has been classified as Likely benign.
Frequency
Consequence
NM_000033.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.2190G>A | p.Pro730= | synonymous_variant | 10/10 | ENST00000218104.6 | |
ABCD1 | XM_047441916.1 | c.2490G>A | p.Pro830= | synonymous_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.2190G>A | p.Pro730= | synonymous_variant | 10/10 | 1 | NM_000033.4 | P1 | |
PLXNB3-AS1 | ENST00000434284.1 | n.72-5109C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000939 AC: 105AN: 111851Hom.: 1 Cov.: 23 AF XY: 0.000822 AC XY: 28AN XY: 34069
GnomAD3 exomes AF: 0.000805 AC: 92AN: 114276Hom.: 1 AF XY: 0.00105 AC XY: 39AN XY: 37190
GnomAD4 exome AF: 0.00128 AC: 1350AN: 1058279Hom.: 1 Cov.: 37 AF XY: 0.00128 AC XY: 440AN XY: 343735
GnomAD4 genome ? AF: 0.000929 AC: 104AN: 111904Hom.: 1 Cov.: 23 AF XY: 0.000820 AC XY: 28AN XY: 34132
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 16, 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing;curation | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 18, 2011 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 01, 2016 | This alteration is classified as likely 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at