chr4-184388899-G-A
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_002199.4(IRF2):c.909C>T(p.Ser303=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,614,068 control chromosomes in the GnomAD database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 83 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 79 hom. )
Consequence
IRF2
NM_002199.4 synonymous
NM_002199.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.73
Genes affected
IRF2 (HGNC:6117): (interferon regulatory factor 2) IRF2 encodes interferon regulatory factor 2, a member of the interferon regulatory transcription factor (IRF) family. IRF2 competitively inhibits the IRF1-mediated transcriptional activation of interferons alpha and beta, and presumably other genes that employ IRF1 for transcription activation. However, IRF2 also functions as a transcriptional activator of histone H4. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 4-184388899-G-A is Benign according to our data. Variant chr4-184388899-G-A is described in ClinVar as [Benign]. Clinvar id is 708814.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.73 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0609 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF2 | NM_002199.4 | c.909C>T | p.Ser303= | synonymous_variant | 9/9 | ENST00000393593.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF2 | ENST00000393593.8 | c.909C>T | p.Ser303= | synonymous_variant | 9/9 | 1 | NM_002199.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0180 AC: 2744AN: 152056Hom.: 84 Cov.: 32
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GnomAD3 exomes AF: 0.00468 AC: 1177AN: 251276Hom.: 39 AF XY: 0.00350 AC XY: 476AN XY: 135826
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GnomAD4 exome AF: 0.00179 AC: 2617AN: 1461894Hom.: 79 Cov.: 30 AF XY: 0.00154 AC XY: 1119AN XY: 727248
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GnomAD4 genome AF: 0.0181 AC: 2751AN: 152174Hom.: 83 Cov.: 32 AF XY: 0.0176 AC XY: 1311AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at