chr2-190995212-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 3P and 13B. PM1PP2BP4_StrongBP6BS1BS2
The ENST00000361099.8(STAT1):āc.793A>Gā(p.Ile265Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000377 in 1,613,848 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000361099.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAT1 | NM_007315.4 | c.793A>G | p.Ile265Val | missense_variant | 10/25 | ENST00000361099.8 | NP_009330.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAT1 | ENST00000361099.8 | c.793A>G | p.Ile265Val | missense_variant | 10/25 | 1 | NM_007315.4 | ENSP00000354394 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00205 AC: 311AN: 151996Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000457 AC: 115AN: 251412Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135876
GnomAD4 exome AF: 0.000203 AC: 297AN: 1461734Hom.: 0 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 727176
GnomAD4 genome AF: 0.00205 AC: 312AN: 152114Hom.: 2 Cov.: 31 AF XY: 0.00198 AC XY: 147AN XY: 74384
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 12, 2022 | BP4, PP2 - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | STAT1: PP2, BP4, BS2 - |
Recurrent infections Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | May 24, 2019 | - - |
STAT1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 10, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Immunodeficiency 31B;C3279990:Autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome;C4013950:Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at