2-171785310-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003705.5(SLC25A12):c.2001G>A(p.Val667=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,032 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 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SLC25A12
NM_003705.5 synonymous
NM_003705.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0250
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 -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 2-171785310-C-T is Benign according to our data. Variant chr2-171785310-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 957870.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.025 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A12 | NM_003705.5 | c.2001G>A | p.Val667= | synonymous_variant | 18/18 | ENST00000422440.7 | |
SLC25A12 | XM_047446142.1 | c.1728G>A | p.Val576= | synonymous_variant | 16/16 | ||
SLC25A12 | NR_047549.2 | n.1915G>A | non_coding_transcript_exon_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A12 | ENST00000422440.7 | c.2001G>A | p.Val667= | synonymous_variant | 18/18 | 1 | NM_003705.5 | P1 | |
SLC25A12 | ENST00000472070.1 | n.1411G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SLC25A12 | ENST00000263812.8 | c.*1621G>A | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727232
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 28, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at