chr12-113002948-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002535.3(OAS2):c.1025C>T(p.Thr342Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,992 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251162Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135716
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461718Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727166
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 31, 2022 | The c.1025C>T (p.T342M) alteration is located in exon 6 (coding exon 6) of the OAS2 gene. This alteration results from a C to T substitution at nucleotide position 1025, causing the threonine (T) at amino acid position 342 to be replaced by a methionine (M). 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