rs2020854
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005419.4(STAT2):c.1257+6A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 1,613,970 control chromosomes in the GnomAD database, including 14,529 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 Benign (★★).
Frequency
Consequence
NM_005419.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAT2 | NM_005419.4 | c.1257+6A>G | splice_region_variant, intron_variant | ENST00000314128.9 | NP_005410.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAT2 | ENST00000314128.9 | c.1257+6A>G | splice_region_variant, intron_variant | 1 | NM_005419.4 | ENSP00000315768.4 |
Frequencies
GnomAD3 genomes AF: 0.195 AC: 29663AN: 151962Hom.: 6111 Cov.: 31
GnomAD3 exomes AF: 0.0894 AC: 22474AN: 251482Hom.: 2801 AF XY: 0.0785 AC XY: 10669AN XY: 135920
GnomAD4 exome AF: 0.0757 AC: 110639AN: 1461890Hom.: 8386 Cov.: 33 AF XY: 0.0730 AC XY: 53104AN XY: 727248
GnomAD4 genome AF: 0.196 AC: 29758AN: 152080Hom.: 6143 Cov.: 31 AF XY: 0.189 AC XY: 14049AN XY: 74344
ClinVar
Submissions by phenotype
Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at