chr13-109782961-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003749.3(IRS2):c.3093G>A(p.Pro1031=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00945 in 1,426,174 control chromosomes in the GnomAD database, including 89 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0065 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0098 ( 83 hom. )
Consequence
IRS2
NM_003749.3 synonymous
NM_003749.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.573
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 13-109782961-C-T is Benign according to our data. Variant chr13-109782961-C-T is described in ClinVar as [Benign]. Clinvar id is 770424.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.573 with no splicing effect.
BS2
?
High AC in GnomAd at 982 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRS2 | NM_003749.3 | c.3093G>A | p.Pro1031= | synonymous_variant | 1/2 | ENST00000375856.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRS2 | ENST00000375856.5 | c.3093G>A | p.Pro1031= | synonymous_variant | 1/2 | 1 | NM_003749.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00648 AC: 982AN: 151582Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.00723 AC: 340AN: 47038Hom.: 3 AF XY: 0.00824 AC XY: 219AN XY: 26578
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GnomAD4 exome AF: 0.00980 AC: 12495AN: 1274484Hom.: 83 Cov.: 54 AF XY: 0.00987 AC XY: 6165AN XY: 624866
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GnomAD4 genome ? AF: 0.00648 AC: 983AN: 151690Hom.: 6 Cov.: 33 AF XY: 0.00608 AC XY: 451AN XY: 74146
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational 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