3-48857132-TAA-TAAAA
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_000387.6(SLC25A20):c.*576_*577dupTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 146,260 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00038 ( 0 hom. )
Consequence
SLC25A20
NM_000387.6 3_prime_UTR
NM_000387.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.539
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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000387.6. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC25A20 | TSL:1 MANE Select | c.*576_*577dupTT | 3_prime_UTR | Exon 9 of 9 | ENSP00000326305.4 | O43772 | |||
| SLC25A20 | c.*576_*577dupTT | 3_prime_UTR | Exon 9 of 9 | ENSP00000550936.1 | |||||
| SLC25A20 | c.*576_*577dupTT | 3_prime_UTR | Exon 7 of 7 | ENSP00000550937.1 |
Frequencies
GnomAD3 genomes 0.00000696 AC: 1AN: 143660Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
143660
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000385 AC: 1AN: 2600Hom.: 0 Cov.: 0 AF XY: 0.000734 AC XY: 1AN XY: 1362 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
1
AN:
2600
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
1362
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
14
American (AMR)
AF:
AC:
0
AN:
660
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12
East Asian (EAS)
AF:
AC:
0
AN:
40
South Asian (SAS)
AF:
AC:
0
AN:
240
European-Finnish (FIN)
AF:
AC:
0
AN:
10
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1530
Other (OTH)
AF:
AC:
0
AN:
94
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
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
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000696 AC: 1AN: 143660Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 69574 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
143660
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
69574
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
39292
American (AMR)
AF:
AC:
0
AN:
14262
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
3388
East Asian (EAS)
AF:
AC:
0
AN:
4970
South Asian (SAS)
AF:
AC:
0
AN:
4538
European-Finnish (FIN)
AF:
AC:
0
AN:
8812
Middle Eastern (MID)
AF:
AC:
0
AN:
306
European-Non Finnish (NFE)
AF:
AC:
0
AN:
65256
Other (OTH)
AF:
AC:
0
AN:
1944
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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