22-19177751-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_005984.5(SLC25A1):c.417C>T(p.Val139=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V139V) has been classified as Likely benign.
Frequency
Consequence
NM_005984.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A1 | NM_005984.5 | c.417C>T | p.Val139= | synonymous_variant | 4/9 | ENST00000215882.10 | |
SLC25A1 | NM_001256534.2 | c.438C>T | p.Val146= | synonymous_variant | 3/8 | ||
SLC25A1 | NM_001287387.2 | c.108C>T | p.Val36= | synonymous_variant | 4/9 | ||
SLC25A1 | NR_046298.3 | n.365+191C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A1 | ENST00000215882.10 | c.417C>T | p.Val139= | synonymous_variant | 4/9 | 1 | NM_005984.5 | P1 | |
SLC25A1 | ENST00000451283.5 | c.108C>T | p.Val36= | synonymous_variant | 4/9 | 2 | |||
SLC25A1 | ENST00000461267.1 | n.563C>T | non_coding_transcript_exon_variant | 3/6 | 3 | ||||
SLC25A1 | ENST00000470922.5 | n.559C>T | non_coding_transcript_exon_variant | 3/8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at