X-153736079-C-G

Variant names:

• chrX-153736079-C-G
• rs782720354
• NM_000033.4:c.1082-33C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000033.4(ABCD1):​c.1082-33C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000092 in 1,086,379 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 9.2e-7 (0 hom. 0 hem.)
• Consequence: ABCD1 NM_000033.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 0 publications found

Genes affected

ABCD1 (HGNC:61): (ATP binding cassette subfamily D member 1) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ALD subfamily, which is involved in peroxisomal import of fatty acids and/or fatty acyl-CoAs in the organelle. All known peroxisomal ABC transporters are half transporters which require a partner half transporter molecule to form a functional homodimeric or heterodimeric transporter. This peroxisomal membrane protein is likely involved in the peroxisomal transport or catabolism of very long chain fatty acids. Defects in this gene have been identified as the underlying cause of adrenoleukodystrophy, an X-chromosome recessively inherited demyelinating disorder of the nervous system. [provided by RefSeq, Jul 2008]

PLXNB3-AS1 (HGNC:40454): (PLXNB3 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000033.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCD1	NM_000033.4	MANE Select	c.1082-33C>G		intron	N/A	NP_000024.2
	ABCD1	NM_001440747.1		c.1082-33C>G		intron	N/A	NP_001427676.1
	PLXNB3-AS1	NR_199693.1		n.2589G>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCD1	ENST00000218104.6	TSL:1 MANE Select	c.1082-33C>G		intron	N/A	ENSP00000218104.3	P33897
	ABCD1	ENST00000862307.1		c.1082-33C>G		intron	N/A	ENSP00000532366.1
	ABCD1	ENST00000862306.1		c.1082-33C>G		intron	N/A	ENSP00000532365.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 9.20e-7 AC: 1 AN: 1086379 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 354107

African (AFR) AF: 0.00 AC: 0 AN: 26159

American (AMR) AF: 0.00 AC: 0 AN: 35056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19253

East Asian (EAS) AF: 0.00 AC: 0 AN: 30027

South Asian (SAS) AF: 0.00 AC: 0 AN: 53767

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39202

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3509

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 833832

Other (OTH) AF: 0.0000219 AC: 1 AN: 45574

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.42
PhyloP100		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs782720354; hg19: chrX-153001533;