chr2-226799185-C-T
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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.-447G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 1,105,064 control chromosomes in the GnomAD database, including 4,613 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 0.13 ( 2609 hom., cov: 32)
Exomes 𝑓: 0.038 ( 2004 hom. )
Consequence
IRS1
NM_005544.3 5_prime_UTR
NM_005544.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.648
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=-0.54).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRS1 | NM_005544.3 | c.-447G>A | 5_prime_UTR_variant | 1/2 | ENST00000305123.6 | NP_005535.1 | ||
IRS1 | XM_047444223.1 | c.-447G>A | 5_prime_UTR_variant | 1/2 | XP_047300179.1 | |||
IRS1 | XM_047444224.1 | c.-447G>A | 5_prime_UTR_variant | 1/2 | XP_047300180.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRS1 | ENST00000305123.6 | c.-447G>A | 5_prime_UTR_variant | 1/2 | 1 | NM_005544.3 | ENSP00000304895 | P1 |
Frequencies
GnomAD3 genomes AF: 0.129 AC: 19549AN: 151852Hom.: 2603 Cov.: 32
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GnomAD4 exome AF: 0.0377 AC: 35928AN: 953094Hom.: 2004 Cov.: 34 AF XY: 0.0390 AC XY: 17515AN XY: 449478
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GnomAD4 genome AF: 0.129 AC: 19579AN: 151970Hom.: 2609 Cov.: 32 AF XY: 0.128 AC XY: 9542AN XY: 74284
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ClinVar
Not reported inComputational scores
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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