chr12-121033523-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003733.4(OASL):āc.419T>Cā(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 (ā ). 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