X-153736113-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000033.4(ABCD1):āc.1083T>Cā(p.Asp361Asp) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000917 in 1,090,863 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_000033.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCD1 | NM_000033.4 | c.1083T>C | p.Asp361Asp | splice_region_variant, synonymous_variant | Exon 3 of 10 | ENST00000218104.6 | NP_000024.2 | |
ABCD1 | XM_047441916.1 | c.1083T>C | p.Asp361Asp | splice_region_variant, synonymous_variant | Exon 3 of 11 | XP_047297872.1 | ||
ABCD1 | XM_047441917.1 | c.1083T>C | p.Asp361Asp | splice_region_variant, synonymous_variant | Exon 3 of 8 | XP_047297873.1 | ||
LOC124905226 | XR_007068350.1 | n.4238A>G | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCD1 | ENST00000218104.6 | c.1083T>C | p.Asp361Asp | splice_region_variant, synonymous_variant | Exon 3 of 10 | 1 | NM_000033.4 | ENSP00000218104.3 | ||
ABCD1 | ENST00000443684.2 | n.86T>C | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 6 | 3 | |||||
PLXNB3-AS1 | ENST00000434284.1 | n.581-154A>G | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181628Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67124
GnomAD4 exome AF: 9.17e-7 AC: 1AN: 1090863Hom.: 0 Cov.: 35 AF XY: 0.00000279 AC XY: 1AN XY: 358005
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Adrenoleukodystrophy Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at