12-121033523-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003733.4(OASL):c.419T>C(p.Ile140Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000483 in 1,613,972 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. I140I) has been classified as Likely benign.
Frequency
Consequence
NM_003733.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OASL | NM_003733.4 | c.419T>C | p.Ile140Thr | missense_variant | 2/6 | ENST00000257570.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OASL | ENST00000257570.10 | c.419T>C | p.Ile140Thr | missense_variant | 2/6 | 1 | NM_003733.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000140 AC: 35AN: 250704Hom.: 2 AF XY: 0.000199 AC XY: 27AN XY: 135622
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461888Hom.: 3 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 727244
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.419T>C (p.I140T) alteration is located in exon 2 (coding exon 2) of the OASL gene. This alteration results from a T to C substitution at nucleotide position 419, causing the isoleucine (I) at amino acid position 140 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at