13-40789460-C-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000478827.1(SLC25A15):n.49C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00788 in 151,584 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000478827.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Frequencies
GnomAD3 genomes AF: 0.00788 AC: 1192AN: 151364Hom.: 7 Cov.: 32
GnomAD4 exome AF: 0.0268 AC: 3AN: 112Hom.: 0 Cov.: 0 AF XY: 0.0119 AC XY: 1AN XY: 84
GnomAD4 genome AF: 0.00786 AC: 1191AN: 151472Hom.: 7 Cov.: 32 AF XY: 0.00674 AC XY: 499AN XY: 74028
ClinVar
Submissions by phenotype
not provided Benign:2
SLC25A15: BS1, BS2 -
See Variant Classification Assertion Criteria. -
Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at