rs13431554
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005544.3(IRS1):c.*3400T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,112 control chromosomes in the GnomAD database, including 1,204 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 0.10 ( 1204 hom., cov: 32)
Exomes 𝑓: 0.083 ( 0 hom. )
Consequence
IRS1
NM_005544.3 3_prime_UTR
NM_005544.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.87
Genes affected
IRS1 (HGNC:6125): (insulin receptor substrate 1) This gene encodes a protein which is phosphorylated by insulin receptor tyrosine kinase. Mutations in this gene are associated with type II diabetes and susceptibility to insulin resistance. [provided by RefSeq, Nov 2009]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRS1 | NM_005544.3 | c.*3400T>C | 3_prime_UTR_variant | 2/2 | ENST00000305123.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRS1 | ENST00000305123.6 | c.*3400T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_005544.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15773AN: 151982Hom.: 1199 Cov.: 32
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GnomAD4 exome AF: 0.0833 AC: 1AN: 12Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 1AN XY: 8
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GnomAD4 genome ? AF: 0.104 AC: 15814AN: 152100Hom.: 1204 Cov.: 32 AF XY: 0.104 AC XY: 7720AN XY: 74370
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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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at