rs7545855
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_182972.3(IRF2BP2):c.232T>C(p.Ser78Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 1,377,458 control chromosomes in the GnomAD database, including 352,861 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_182972.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRF2BP2 | NM_182972.3 | c.232T>C | p.Ser78Pro | missense_variant | 1/2 | ENST00000366609.4 | |
IRF2BP2 | NM_001077397.1 | c.232T>C | p.Ser78Pro | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRF2BP2 | ENST00000366609.4 | c.232T>C | p.Ser78Pro | missense_variant | 1/2 | 1 | NM_182972.3 | P3 | |
IRF2BP2 | ENST00000366610.7 | c.232T>C | p.Ser78Pro | missense_variant | 1/2 | 1 | A1 | ||
ENST00000436039.1 | n.631-158A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.728 AC: 109668AN: 150662Hom.: 41000 Cov.: 32
GnomAD3 exomes AF: 0.610 AC: 11605AN: 19032Hom.: 3855 AF XY: 0.611 AC XY: 6810AN XY: 11144
GnomAD4 exome AF: 0.707 AC: 867342AN: 1226686Hom.: 311822 Cov.: 64 AF XY: 0.702 AC XY: 420732AN XY: 599294
GnomAD4 genome ? AF: 0.728 AC: 109756AN: 150772Hom.: 41039 Cov.: 32 AF XY: 0.718 AC XY: 52866AN XY: 73584
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 72% of patients studied by a panel of primary immunodeficiencies. Number of patients: 68. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Immunodeficiency, common variable, 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at