rs79264292
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_005419.4(STAT2):c.285+5T>C variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000283 in 1,613,270 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005419.4 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAT2 | NM_005419.4 | c.285+5T>C | splice_donor_5th_base_variant, intron_variant | ENST00000314128.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAT2 | ENST00000314128.9 | c.285+5T>C | splice_donor_5th_base_variant, intron_variant | 1 | NM_005419.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 235AN: 152110Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000403 AC: 101AN: 250566Hom.: 1 AF XY: 0.000355 AC XY: 48AN XY: 135376
GnomAD4 exome AF: 0.000151 AC: 220AN: 1461042Hom.: 0 Cov.: 32 AF XY: 0.000120 AC XY: 87AN XY: 726752
GnomAD4 genome AF: 0.00156 AC: 237AN: 152228Hom.: 1 Cov.: 31 AF XY: 0.00149 AC XY: 111AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at