chr1-94458490-A-G

Position:

• chr1-94458490-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002858.4(ABCD3):​c.111-117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 870,726 control chromosomes in the GnomAD database, including 82,668 homozygotes. 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: 𝑓 0.36 (11409 hom., cov: 31)
  • Exomes 𝑓: 0.44 (71259 hom.)
• Consequence: ABCD3 NM_002858.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

Genes affected

ABCD3 (HGNC:67): (ATP binding cassette subfamily D member 3) 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 likely plays an important role in peroxisome biogenesis. Mutations have been associated with some forms of Zellweger syndrome, a heterogeneous group of peroxisome assembly disorders. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCD3	NM_002858.4	c.111-117A>G		intron_variant		ENST00000370214.9	NP_002849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCD3	ENST00000370214.9	c.111-117A>G		intron_variant		1	NM_002858.4	ENSP00000359233.4
ABCD3	ENST00000315713.5	c.111-117A>G		intron_variant		1		ENSP00000326880.5
ABCD3	ENST00000647998.2	c.111-117A>G		intron_variant				ENSP00000497921.2
ABCD3	ENST00000468860.1	n.188-117A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54461 AN: 151988 Hom.: 11409 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.432

GnomAD4 exome AF: 0.436 AC: 313072 AN: 718620 Hom.: 71259 AF XY: 0.436 AC XY: 166603 AN XY: 382134

Gnomad4 AFR exome AF: 0.138

Gnomad4 AMR exome AF: 0.386

Gnomad4 ASJ exome AF: 0.451

Gnomad4 EAS exome AF: 0.222

Gnomad4 SAS exome AF: 0.376

Gnomad4 FIN exome AF: 0.365

Gnomad4 NFE exome AF: 0.482

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.358 AC: 54454 AN: 152106 Hom.: 11409 Cov.: 31 AF XY: 0.352 AC XY: 26160 AN XY: 74378

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.425

Alfa AF: 0.426 Hom.: 7215

Bravo AF: 0.356

Asia WGS AF: 0.256 AC: 893 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.1
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs2147794; hg19: chr1-94924046; COSMIC: COSV59865570;