rs1325969667

Variant names:

• chr1-234609336-G-A
• rs1325969667
• NM_182972.3:c.159C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-234609336-G-A
• chr1-234609336-G-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_182972.3(IRF2BP2):​c.159C>T​(p.Ile53Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000725 in 1,379,208 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. I53I) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: IRF2BP2 NM_182972.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 0 publications found

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)

ENSG00000228830 (HGNC:):

ACMG classification

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=1.4 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRF2BP2	NM_182972.3	c.159C>T	p.Ile53Ile	synonymous_variant	Exon 1 of 2	ENST00000366609.4	NP_892017.2
IRF2BP2	NM_001077397.1	c.159C>T	p.Ile53Ile	synonymous_variant	Exon 1 of 2		NP_001070865.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF2BP2	ENST00000366609.4	c.159C>T	p.Ile53Ile	synonymous_variant	Exon 1 of 2	1	NM_182972.3	ENSP00000355568.3
IRF2BP2	ENST00000366610.8	c.159C>T	p.Ile53Ile	synonymous_variant	Exon 1 of 2	1		ENSP00000355569.3
LINC00184	ENST00000796406.1	n.42G>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000228830	ENST00000436039.1	n.631-85G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 7.25e-7 AC: 1 AN: 1379208 Hom.: 0 Cov.: 34 AF XY: 0.00000146 AC XY: 1 AN XY: 683196

African (AFR) AF: 0.00 AC: 0 AN: 28166

American (AMR) AF: 0.00 AC: 0 AN: 34628

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24058

East Asian (EAS) AF: 0.00 AC: 0 AN: 31294

South Asian (SAS) AF: 0.00 AC: 0 AN: 77538

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48516

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4658

European-Non Finnish (NFE) AF: 9.31e-7 AC: 1 AN: 1073584

Other (OTH) AF: 0.00 AC: 0 AN: 56766

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		1.4
PromoterAI		-0.13	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

Other links and lift over

dbSNP: rs1325969667; hg19: chr1-234745082;