rs564026448
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_001191061.2(SLC25A22):c.903C>T(p.Ile301=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,609,464 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 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
SLC25A22
NM_001191061.2 synonymous
NM_001191061.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.571
Genes affected
SLC25A22 (HGNC:19954): (solute carrier family 25 member 22) This gene encodes a mitochondrial glutamate carrier. Mutations in this gene are associated with early infantile epileptic encephalopathy. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 11-791984-G-A is Benign according to our data. Variant chr11-791984-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 530646.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.571 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000394 (6/152356) while in subpopulation EAS AF= 0.000965 (5/5180). AF 95% confidence interval is 0.00038. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A22 | NM_001191061.2 | c.903C>T | p.Ile301= | synonymous_variant | 10/10 | ENST00000628067.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A22 | ENST00000628067.3 | c.903C>T | p.Ile301= | synonymous_variant | 10/10 | 1 | NM_001191061.2 | P1 | |
SLC25A22 | ENST00000320230.9 | c.903C>T | p.Ile301= | synonymous_variant | 10/10 | 1 | P1 | ||
SLC25A22 | ENST00000531214.5 | c.903C>T | p.Ile301= | synonymous_variant | 10/10 | 2 | P1 | ||
SLC25A22 | ENST00000481290.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152238Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000462 AC: 11AN: 238346Hom.: 1 AF XY: 0.0000535 AC XY: 7AN XY: 130854
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1457108Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 724930
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74494
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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