3-48857132-TA-T

Variant names:

• chr3-48857132-TA-T
• rs533476473
• NM_000387.6:c.*577delT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000387.6(SLC25A20):​c.*577delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00243 in 145,974 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., cov: 31)
  • Exomes 𝑓: 0.065 (0 hom.)
• Consequence: SLC25A20 NM_000387.6 3_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.539

Genes affected

SLC25A20 (HGNC:1421): (solute carrier family 25 member 20) This gene product is one of several closely related mitochondrial-membrane carrier proteins that shuttle substrates between cytosol and the intramitochondrial matrix space. This protein mediates the transport of acylcarnitines into mitochondrial matrix for their oxidation by the mitochondrial fatty acid-oxidation pathway. Mutations in this gene are associated with carnitine-acylcarnitine translocase deficiency, which can cause a variety of pathological conditions such as hypoglycemia, cardiac arrest, hepatomegaly, hepatic dysfunction and muscle weakness, and is usually lethal in new born and infants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A20	NM_000387.6	c.*577delT		3_prime_UTR_variant	Exon 9 of 9	ENST00000319017.5	NP_000378.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A20	ENST00000319017	c.*577delT		3_prime_UTR_variant	Exon 9 of 9	1	NM_000387.6	ENSP00000326305.4
SLC25A20	ENST00000430379	c.*577delT		3_prime_UTR_variant	Exon 7 of 7	3		ENSP00000388986.1
SLC25A20	ENST00000479050.1	n.*108delT		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.00133 AC: 191 AN: 143432 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00119

Gnomad ASJ AF: 0.000591

Gnomad EAS AF: 0.000604

Gnomad SAS AF: 0.00353

Gnomad FIN AF: 0.00263

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000767

Gnomad OTH AF: 0.00155

GnomAD4 exome AF: 0.0651 AC: 163 AN: 2502 Hom.: 0 Cov.: 0 AF XY: 0.0620 AC XY: 81 AN XY: 1306

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0540

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0526

Gnomad4 SAS exome AF: 0.0517

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0740

Gnomad4 OTH exome AF: 0.0638

GnomAD4 genome AF: 0.00133 AC: 191 AN: 143472 Hom.: 1 Cov.: 31 AF XY: 0.00144 AC XY: 100 AN XY: 69516

Gnomad4 AFR AF: 0.00196

Gnomad4 AMR AF: 0.00119

Gnomad4 ASJ AF: 0.000591

Gnomad4 EAS AF: 0.000606

Gnomad4 SAS AF: 0.00354

Gnomad4 FIN AF: 0.00263

Gnomad4 NFE AF: 0.000767

Gnomad4 OTH AF: 0.00154

Alfa AF: 0.000325 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Carnitine acylcarnitine translocase deficiency Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

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: rs533476473; hg19: chr3-48894565;