chr18-45625824-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007163.4(SLC14A2):c.292C>A(p.Leu98Ile) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L98F) has been classified as Uncertain significance.
Frequency
Consequence
NM_007163.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC14A2 | ENST00000255226.11 | c.292C>A | p.Leu98Ile | missense_variant | Exon 3 of 20 | 1 | NM_007163.4 | ENSP00000255226.5 | ||
SLC14A2 | ENST00000586448.5 | c.292C>A | p.Leu98Ile | missense_variant | Exon 4 of 21 | 2 | ENSP00000465953.1 | |||
SLC14A2 | ENST00000323329.3 | n.292C>A | non_coding_transcript_exon_variant | Exon 3 of 11 | 2 | ENSP00000320689.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000568 AC: 1AN: 175970Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 97316
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1356920Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 668854
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at