22-19176262-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_005984.5(SLC25A1):c.822-18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,509,666 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 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
SLC25A1
NM_005984.5 intron
NM_005984.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.03
Genes affected
SLC25A1 (HGNC:10979): (solute carrier family 25 member 1) This gene encodes a member of the mitochondrial carrier subfamily of solute carrier proteins. Members of this family include nuclear-encoded transporters that translocate small metabolites across the mitochondrial membrane. This protein regulates the movement of citrate across the inner membranes of the mitochondria. Mutations in this gene have been associated with combined D-2- and L-2-hydroxyglutaric aciduria. Pseudogenes of this gene have been identified on chromosomes 7, 11, 16, and 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 22-19176262-C-T is Benign according to our data. Variant chr22-19176262-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 511598.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.822-18G>A | intron_variant | ENST00000215882.10 | |||
SLC25A1 | NM_001256534.2 | c.843-18G>A | intron_variant | ||||
SLC25A1 | NM_001287387.2 | c.513-18G>A | intron_variant | ||||
SLC25A1 | NR_046298.3 | n.746-18G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.822-18G>A | intron_variant | 1 | NM_005984.5 | P1 | |||
SLC25A1 | ENST00000451283.5 | c.513-18G>A | intron_variant | 2 | |||||
SLC25A1 | ENST00000470922.5 | n.964-18G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248964Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134976
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GnomAD4 exome AF: 0.0000199 AC: 27AN: 1357824Hom.: 0 Cov.: 27 AF XY: 0.0000162 AC XY: 11AN XY: 680992
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74176
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 05, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 19, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at