chr2-171785269-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003705.5(SLC25A12):c.*5A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,016 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: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
SLC25A12
NM_003705.5 3_prime_UTR
NM_003705.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.221
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 2-171785269-T-C is Benign according to our data. Variant chr2-171785269-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3049843.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A12 | NM_003705.5 | c.*5A>G | 3_prime_UTR_variant | 18/18 | ENST00000422440.7 | ||
SLC25A12 | XM_047446142.1 | c.*5A>G | 3_prime_UTR_variant | 16/16 | |||
SLC25A12 | NR_047549.2 | n.1956A>G | non_coding_transcript_exon_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A12 | ENST00000422440.7 | c.*5A>G | 3_prime_UTR_variant | 18/18 | 1 | NM_003705.5 | P1 | ||
SLC25A12 | ENST00000472070.1 | n.1452A>G | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SLC25A12 | ENST00000263812.8 | c.*1662A>G | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251402Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727174
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GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC25A12-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at