rs11156606

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000218104.6(ABCD1):​c.1780+322A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 112,144 control chromosomes in the GnomAD database, including 4,981 homozygotes. There are 8,590 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 4981 hom., 8590 hem., cov: 24)

Consequence

ABCD1
ENST00000218104.6 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.29
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
Variant X-153741041-A-C is Benign according to our data. Variant chrX-153741041-A-C is described in ClinVar as [Benign]. Clinvar id is 1293829.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ABCD1NM_000033.4 linkuse as main transcriptc.1780+322A>C intron_variant ENST00000218104.6 NP_000024.2
LOC124905226XR_007068350.1 linkuse as main transcriptn.507T>G non_coding_transcript_exon_variant 1/2
ABCD1XM_047441916.1 linkuse as main transcriptc.2080+322A>C intron_variant XP_047297872.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ABCD1ENST00000218104.6 linkuse as main transcriptc.1780+322A>C intron_variant 1 NM_000033.4 ENSP00000218104 P1
PLXNB3-AS1ENST00000434284.1 linkuse as main transcriptn.72-2463T>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.262
AC:
29371
AN:
112088
Hom.:
4970
Cov.:
24
AF XY:
0.249
AC XY:
8543
AN XY:
34282
show subpopulations
Gnomad AFR
AF:
0.640
Gnomad AMI
AF:
0.0366
Gnomad AMR
AF:
0.131
Gnomad ASJ
AF:
0.0694
Gnomad EAS
AF:
0.0871
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.110
Gnomad MID
AF:
0.0917
Gnomad NFE
AF:
0.119
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.262
AC:
29433
AN:
112144
Hom.:
4981
Cov.:
24
AF XY:
0.250
AC XY:
8590
AN XY:
34348
show subpopulations
Gnomad4 AFR
AF:
0.641
Gnomad4 AMR
AF:
0.130
Gnomad4 ASJ
AF:
0.0694
Gnomad4 EAS
AF:
0.0871
Gnomad4 SAS
AF:
0.155
Gnomad4 FIN
AF:
0.110
Gnomad4 NFE
AF:
0.119
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.188
Hom.:
1565
Bravo
AF:
0.281

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 06, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.5
DANN
Benign
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11156606; hg19: chrX-153006495; API