13-40793160-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014252.4(SLC25A15):c.-67A>T variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00745 in 1,524,934 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014252.4 splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A15 | NM_014252.4 | c.-67A>T | splice_region_variant | 2/7 | ENST00000338625.9 | NP_055067.1 | ||
SLC25A15 | NM_014252.4 | c.-67A>T | 5_prime_UTR_variant | 2/7 | ENST00000338625.9 | NP_055067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A15 | ENST00000338625.9 | c.-67A>T | splice_region_variant | 2/7 | 1 | NM_014252.4 | ENSP00000342267.4 | |||
SLC25A15 | ENST00000338625 | c.-67A>T | 5_prime_UTR_variant | 2/7 | 1 | NM_014252.4 | ENSP00000342267.4 |
Frequencies
GnomAD3 genomes AF: 0.00602 AC: 916AN: 152176Hom.: 2 Cov.: 32
GnomAD4 exome AF: 0.00761 AC: 10441AN: 1372640Hom.: 43 Cov.: 20 AF XY: 0.00738 AC XY: 5077AN XY: 687846
GnomAD4 genome AF: 0.00601 AC: 916AN: 152294Hom.: 2 Cov.: 32 AF XY: 0.00579 AC XY: 431AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 15, 2021 | - - |
Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at