rs13003121
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016133.4(INSIG2):c.637-43G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 1,355,860 control chromosomes in the GnomAD database, including 910 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 0.043 ( 201 hom., cov: 33)
Exomes 𝑓: 0.031 ( 709 hom. )
Consequence
INSIG2
NM_016133.4 intron
NM_016133.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.350
Genes affected
INSIG2 (HGNC:20452): (insulin induced gene 2) The protein encoded by this gene is highly similar to the protein product encoded by gene INSIG1. Both INSIG1 protein and this protein are endoplasmic reticulum proteins that block the processing of sterol regulatory element binding proteins (SREBPs) by binding to SREBP cleavage-activating protein (SCAP), and thus prevent SCAP from escorting SREBPs to the Golgi. [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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.081 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INSIG2 | NM_016133.4 | c.637-43G>A | intron_variant | ENST00000245787.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSIG2 | ENST00000245787.9 | c.637-43G>A | intron_variant | 1 | NM_016133.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0432 AC: 6575AN: 152114Hom.: 202 Cov.: 33
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GnomAD3 exomes AF: 0.0256 AC: 5374AN: 209930Hom.: 101 AF XY: 0.0235 AC XY: 2696AN XY: 114602
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GnomAD4 exome AF: 0.0305 AC: 36744AN: 1203628Hom.: 709 Cov.: 17 AF XY: 0.0294 AC XY: 17912AN XY: 609722
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GnomAD4 genome ? AF: 0.0432 AC: 6578AN: 152232Hom.: 201 Cov.: 33 AF XY: 0.0405 AC XY: 3015AN XY: 74434
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at