chr3-48891971-T-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000387.6(SLC25A20):c.198+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000689 in 1,452,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
SLC25A20
NM_000387.6 intron
NM_000387.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00500
Publications
0 publications found
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]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-48891971-T-C is Benign according to our data. Variant chr3-48891971-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 571525.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SLC25A20 | NM_000387.6 | c.198+9A>G | intron_variant | Intron 2 of 8 | ENST00000319017.5 | NP_000378.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SLC25A20 | ENST00000319017.5 | c.198+9A>G | intron_variant | Intron 2 of 8 | 1 | NM_000387.6 | ENSP00000326305.4 | |||
| SLC25A20 | ENST00000430379.5 | c.198+9A>G | intron_variant | Intron 2 of 6 | 3 | ENSP00000388986.1 | ||||
| SLC25A20 | ENST00000440964.1 | n.*28+9A>G | intron_variant | Intron 3 of 9 | 2 | ENSP00000388563.1 | ||||
| PRKAR2A-AS1 | ENST00000721545.1 | n.397-5420T>C | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1452338Hom.: 0 Cov.: 29 AF XY: 0.00000553 AC XY: 4AN XY: 723174 show subpopulations
GnomAD4 exome
AF:
AC:
10
AN:
1452338
Hom.:
Cov.:
29
AF XY:
AC XY:
4
AN XY:
723174
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33296
American (AMR)
AF:
AC:
0
AN:
44690
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26084
East Asian (EAS)
AF:
AC:
0
AN:
39596
South Asian (SAS)
AF:
AC:
0
AN:
86062
European-Finnish (FIN)
AF:
AC:
0
AN:
53398
Middle Eastern (MID)
AF:
AC:
0
AN:
5744
European-Non Finnish (NFE)
AF:
AC:
10
AN:
1103410
Other (OTH)
AF:
AC:
0
AN:
60058
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
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55-60
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Carnitine acylcarnitine translocase deficiency Benign:1
Jan 13, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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