GeneBe

1-234609309-C-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_182972.3(IRF2BP2):​c.186G>C​(p.Ala62Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,348,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A62A) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 7.4e-7 ( 0 hom. )

Consequence

IRF2BP2
NM_182972.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.227

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)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP7
Synonymous conserved (PhyloP=-0.227 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRF2BP2NM_182972.3 linkc.186G>C p.Ala62Ala synonymous_variant Exon 1 of 2 ENST00000366609.4 NP_892017.2 Q7Z5L9-1
IRF2BP2NM_001077397.1 linkc.186G>C p.Ala62Ala 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.186G>C p.Ala62Ala synonymous_variant Exon 1 of 2 1 NM_182972.3 ENSP00000355568.3 Q7Z5L9-1
IRF2BP2ENST00000366610.8 linkc.186G>C p.Ala62Ala synonymous_variant Exon 1 of 2 1 ENSP00000355569.3 Q7Z5L9-2
LINC00184ENST00000796406.1 linkn.15C>G non_coding_transcript_exon_variant Exon 1 of 4
ENSG00000228830ENST00000436039.1 linkn.631-112C>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
7.42e-7
AC:
1
AN:
1348068
Hom.:
0
Cov.:
34
AF XY:
0.00000150
AC XY:
1
AN XY:
665678
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
27310
American (AMR)
AF:
0.00
AC:
0
AN:
29776
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23486
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29442
South Asian (SAS)
AF:
0.0000134
AC:
1
AN:
74674
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46658
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4212
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1057098
Other (OTH)
AF:
0.00
AC:
0
AN:
55412
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
CADD
Benign
12
DANN
Benign
0.74
PhyloP100
-0.23
PromoterAI
0.064
Neutral
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: rs371250654; hg19: chr1-234745055; API