chr2-171785280-AGTGGCTGCCACTGCTGCCTTTGGCTGAACCACAGCAACACTAGGAGACTTAAATTTCGGGAGATAAAGGCCAAATTTGTTTTCGATGCCTGCAAAC-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_003705.5(SLC25A12):c.1935_2030del(p.Phe646_Thr677del) variant causes a inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T645T) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
SLC25A12
NM_003705.5 inframe_deletion
NM_003705.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.18
Genes affected
SLC25A12 (HGNC:10982): (solute carrier family 25 member 12) This gene encodes a calcium-binding mitochondrial carrier protein. The encoded protein localizes to the mitochondria and is involved in the exchange of aspartate for glutamate across the inner mitochondrial membrane. Polymorphisms in this gene may be associated with autism, and mutations in this gene may also be a cause of global cerebral hypomyelination. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_003705.5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A12 | NM_003705.5 | c.1935_2030del | p.Phe646_Thr677del | inframe_deletion | 18/18 | ENST00000422440.7 | |
SLC25A12 | XM_047446142.1 | c.1662_1757del | p.Phe555_Thr586del | inframe_deletion | 16/16 | ||
SLC25A12 | NR_047549.2 | n.1849_1944del | non_coding_transcript_exon_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A12 | ENST00000422440.7 | c.1935_2030del | p.Phe646_Thr677del | inframe_deletion | 18/18 | 1 | NM_003705.5 | P1 | |
SLC25A12 | ENST00000472070.1 | n.1345_1440del | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SLC25A12 | ENST00000263812.8 | c.*1555_*1650del | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2021 | This variant is not present in population databases (ExAC no frequency). This variant, c.1935_2030del, results in the deletion of 32 amino acid(s) of the SLC25A12 protein (p.Phe646_Thr677del), but otherwise preserves the integrity of the reading frame. This variant has not been reported in the literature in individuals with SLC25A12-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.