rs41275080
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003749.3(IRS2):c.*1820A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0631 in 200,156 control chromosomes in the GnomAD database, including 1,694 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.079 ( 1594 hom., cov: 33)
Exomes 𝑓: 0.016 ( 100 hom. )
Consequence
IRS2
NM_003749.3 3_prime_UTR
NM_003749.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0650
Genes affected
IRS2 (HGNC:6126): (insulin receptor substrate 2) This gene encodes the insulin receptor substrate 2, a cytoplasmic signaling molecule that mediates effects of insulin, insulin-like growth factor 1, and other cytokines by acting as a molecular adaptor between diverse receptor tyrosine kinases and downstream effectors. The product of this gene is phosphorylated by the insulin receptor tyrosine kinase upon receptor stimulation, as well as by an interleukin 4 receptor-associated kinase in response to IL4 treatment. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRS2 | NM_003749.3 | c.*1820A>G | 3_prime_UTR_variant | 2/2 | ENST00000375856.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRS2 | ENST00000375856.5 | c.*1820A>G | 3_prime_UTR_variant | 2/2 | 1 | NM_003749.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0793 AC: 11764AN: 148368Hom.: 1592 Cov.: 33
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GnomAD4 exome AF: 0.0162 AC: 839AN: 51670Hom.: 100 Cov.: 0 AF XY: 0.0140 AC XY: 337AN XY: 24060
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GnomAD4 genome ? AF: 0.0794 AC: 11788AN: 148486Hom.: 1594 Cov.: 33 AF XY: 0.0757 AC XY: 5465AN XY: 72202
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at