3-48857132-T-TA

Position:

• chr3-48857132-T-TA

Variant summary

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

The NM_000387.6(SLC25A20):​c.*577_*578insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 146,056 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00064 (0 hom., cov: 31)
  • Exomes 𝑓: 0.082 (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 = 0.0783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A20	NM_000387.6	c.*577_*578insT		3_prime_UTR_variant	9/9	ENST00000319017.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A20	ENST00000319017.5	c.*577_*578insT		3_prime_UTR_variant	9/9	1	NM_000387.6	P1
SLC25A20	ENST00000430379.5	c.*577_*578insT		3_prime_UTR_variant	7/7	3

Frequencies

GnomAD3 genomes AF: 0.000641 AC: 92 AN: 143480 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000815

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000281

Gnomad ASJ AF: 0.000295

Gnomad EAS AF: 0.000604

Gnomad SAS AF: 0.00110

Gnomad FIN AF: 0.00137

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000506

Gnomad OTH AF: 0.00103

GnomAD4 exome AF: 0.0817 AC: 207 AN: 2534 Hom.: 0 Cov.: 0 AF XY: 0.0837 AC XY: 111 AN XY: 1326

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0672

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.0750

Gnomad4 SAS exome AF: 0.0684

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0907

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.000641 AC: 92 AN: 143522 Hom.: 0 Cov.: 31 AF XY: 0.000748 AC XY: 52 AN XY: 69550

Gnomad4 AFR AF: 0.000813

Gnomad4 AMR AF: 0.000280

Gnomad4 ASJ AF: 0.000295

Gnomad4 EAS AF: 0.000606

Gnomad4 SAS AF: 0.000885

Gnomad4 FIN AF: 0.00137

Gnomad4 NFE AF: 0.000506

Gnomad4 OTH AF: 0.00102

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Carnitine acylcarnitine translocase deficiency Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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;