rs2066815
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PP2PP3BP6_Very_StrongBA1
The NM_005419.4(STAT2):c.1343C>T(p.Thr448Met) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00416 in 1,614,200 control chromosomes in the GnomAD database, including 366 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T448T) has been classified as Uncertain significance.
Frequency
Consequence
NM_005419.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAT2 | NM_005419.4 | c.1343C>T | p.Thr448Met | missense_variant, splice_region_variant | 16/24 | ENST00000314128.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAT2 | ENST00000314128.9 | c.1343C>T | p.Thr448Met | missense_variant, splice_region_variant | 16/24 | 1 | NM_005419.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00700 AC: 1065AN: 152192Hom.: 43 Cov.: 31
GnomAD3 exomes AF: 0.0167 AC: 4198AN: 251438Hom.: 259 AF XY: 0.0123 AC XY: 1677AN XY: 135898
GnomAD4 exome AF: 0.00386 AC: 5642AN: 1461890Hom.: 319 Cov.: 32 AF XY: 0.00322 AC XY: 2345AN XY: 727246
GnomAD4 genome ? AF: 0.00706 AC: 1075AN: 152310Hom.: 47 Cov.: 31 AF XY: 0.00693 AC XY: 516AN XY: 74462
ClinVar
Submissions by phenotype
Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 22% of patients studied by a panel of primary immunodeficiencies. Number of patients: 19. Only high quality variants are reported. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at