2-191031078-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_003151.4(STAT4):c.2114G>A(p.Arg705Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003151.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAT4 | NM_003151.4 | c.2114G>A | p.Arg705Gln | missense_variant, splice_region_variant | 23/24 | ENST00000392320.7 | NP_003142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAT4 | ENST00000392320.7 | c.2114G>A | p.Arg705Gln | missense_variant, splice_region_variant | 23/24 | 1 | NM_003151.4 | ENSP00000376134.2 | ||
STAT4 | ENST00000358470.8 | c.2114G>A | p.Arg705Gln | missense_variant, splice_region_variant | 23/24 | 1 | ENSP00000351255.4 | |||
STAT4-AS1 | ENST00000429796.1 | n.328C>T | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
STAT4-AS1 | ENST00000456176.5 | n.224C>T | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251234Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135766
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461552Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 727078
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74256
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 05, 2023 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 705 of the STAT4 protein (p.Arg705Gln). This variant is present in population databases (rs370218298, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with STAT4-related conditions. ClinVar contains an entry for this variant (Variation ID: 2180503). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at