rs776001564

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_182972.3(IRF2BP2):​c.117C>T​(p.Gly39Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000822 in 1,557,122 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: 𝑓 0.000046 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000086 ( 0 hom. )

Consequence

IRF2BP2
NM_182972.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.32

Publications

0 publications found
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]
LINC00184 (HGNC:37192): (long intergenic non-protein coding RNA 184)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 1-234609378-G-A is Benign according to our data. Variant chr1-234609378-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1979845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.32 with no splicing effect.
BS2
High AC in GnomAd4 at 7 AD,Unknown gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRF2BP2NM_182972.3 linkc.117C>T p.Gly39Gly synonymous_variant Exon 1 of 2 ENST00000366609.4 NP_892017.2 Q7Z5L9-1
IRF2BP2NM_001077397.1 linkc.117C>T p.Gly39Gly 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.117C>T p.Gly39Gly synonymous_variant Exon 1 of 2 1 NM_182972.3 ENSP00000355568.3 Q7Z5L9-1
IRF2BP2ENST00000366610.8 linkc.117C>T p.Gly39Gly synonymous_variant Exon 1 of 2 1 ENSP00000355569.3 Q7Z5L9-2
LINC00184ENST00000796406.1 linkn.84G>A non_coding_transcript_exon_variant Exon 1 of 4
ENSG00000228830ENST00000436039.1 linkn.631-43G>A intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.0000462
AC:
7
AN:
151364
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000497
AC:
9
AN:
181198
AF XY:
0.0000494
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000884
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000861
AC:
121
AN:
1405758
Hom.:
0
Cov.:
34
AF XY:
0.0000759
AC XY:
53
AN XY:
697940
show subpopulations
African (AFR)
AF:
0.0000344
AC:
1
AN:
29042
American (AMR)
AF:
0.00
AC:
0
AN:
38834
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24686
East Asian (EAS)
AF:
0.00
AC:
0
AN:
33412
South Asian (SAS)
AF:
0.000137
AC:
11
AN:
80302
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49972
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5212
European-Non Finnish (NFE)
AF:
0.0000985
AC:
107
AN:
1086494
Other (OTH)
AF:
0.0000346
AC:
2
AN:
57804
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
6
12
17
23
29
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0000462
AC:
7
AN:
151364
Hom.:
0
Cov.:
30
AF XY:
0.0000271
AC XY:
2
AN XY:
73926
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
41346
American (AMR)
AF:
0.00
AC:
0
AN:
15212
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5148
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10238
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.000103
AC:
7
AN:
67816
Other (OTH)
AF:
0.00
AC:
0
AN:
2078
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.482
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000416

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Jan 08, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

IRF2BP2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
14
DANN
Benign
0.89
PhyloP100
3.3
PromoterAI
0.043
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.3
Mutation Taster
=100/0
polymorphism

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

Other links and lift over

dbSNP: rs776001564; hg19: chr1-234745124; API