1-234609333-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS2

The NM_182972.3(IRF2BP2):​c.162G>A​(p.Glu54Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000363 in 1,377,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

IRF2BP2
NM_182972.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.616
Variant links:
Genes affected
IRF2BP2 (HGNC:21729): (interferon regulatory factor 2 binding protein 2) This gene encodes an interferon regulatory factor-2 (IRF2) binding protein that interacts with the C-terminal transcriptional repression domain of IRF2. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 1-234609333-C-T is Benign according to our data. Variant chr1-234609333-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2052216.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.616 with no splicing effect.
BS2
High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRF2BP2NM_182972.3 linkc.162G>A p.Glu54Glu synonymous_variant Exon 1 of 2 ENST00000366609.4 NP_892017.2 Q7Z5L9-1
IRF2BP2NM_001077397.1 linkc.162G>A p.Glu54Glu synonymous_variant Exon 1 of 2 NP_001070865.1 Q7Z5L9-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IRF2BP2ENST00000366609.4 linkc.162G>A p.Glu54Glu synonymous_variant Exon 1 of 2 1 NM_182972.3 ENSP00000355568.3 Q7Z5L9-1
IRF2BP2ENST00000366610.7 linkc.162G>A p.Glu54Glu synonymous_variant Exon 1 of 2 1 ENSP00000355569.3 Q7Z5L9-2
ENSG00000228830ENST00000436039.1 linkn.631-88C>T intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000363
AC:
5
AN:
1377342
Hom.:
0
Cov.:
34
AF XY:
0.00000293
AC XY:
2
AN XY:
682158
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000466
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 17, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
10
DANN
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1479179719; hg19: chr1-234745079; API