12-53105173-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003578.4(SOAT2):c.205C>T(p.Arg69Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000022 in 1,589,286 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R69G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003578.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
SOAT2 | ENST00000301466.8 | c.205C>T | p.Arg69Trp | missense_variant | Exon 3 of 15 | 1 | NM_003578.4 | ENSP00000301466.3 | ||
SOAT2 | ENST00000551896.5 | c.205C>T | p.Arg69Trp | missense_variant | Exon 3 of 5 | 2 | ENSP00000450120.1 | |||
SOAT2 | ENST00000542365.1 | n.205C>T | non_coding_transcript_exon_variant | Exon 3 of 14 | 2 | ENSP00000442234.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152038Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000142 AC: 3AN: 211732Hom.: 0 AF XY: 0.00000880 AC XY: 1AN XY: 113680
GnomAD4 exome AF: 0.0000216 AC: 31AN: 1437248Hom.: 0 Cov.: 32 AF XY: 0.0000154 AC XY: 11AN XY: 712754
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152038Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74260
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at