11-2159542-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001042376.3(INS-IGF2):c.187+1243G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,174 control chromosomes in the GnomAD database, including 2,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 2388 hom., cov: 33)
Consequence
INS-IGF2
NM_001042376.3 intron
NM_001042376.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.74
Genes affected
INS-IGF2 (HGNC:33527): (INS-IGF2 readthrough) This locus includes two alternatively spliced read-through transcript variants which align to the INS gene in the 5' region and to the IGF2 gene in the 3' region. One transcript is predicted to encode a protein which shares the N-terminus with the INS protein but has a distinct and longer C-terminus, whereas the other transcript is a candidate for nonsense-mediated decay (NMD). The transcripts are imprinted and are paternally expressed in the limb and eye. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 11-2159542-C-T is Benign according to our data. Variant chr11-2159542-C-T is described in ClinVar as [Benign]. Clinvar id is 1269776.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
INS-IGF2 | NM_001042376.3 | c.187+1243G>A | intron_variant | NP_001035835.1 | ||||
INS-IGF2 | NR_003512.4 | n.246+1243G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INS-IGF2 | ENST00000397270.1 | c.187+1243G>A | intron_variant | 1 | ENSP00000380440.1 | |||||
INS-IGF2 | ENST00000356578.8 | n.187+1243G>A | intron_variant | 5 | ENSP00000348986.4 |
Frequencies
GnomAD3 genomes AF: 0.171 AC: 26005AN: 152056Hom.: 2386 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.171 AC: 26004AN: 152174Hom.: 2388 Cov.: 33 AF XY: 0.165 AC XY: 12304AN XY: 74380
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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 | GeneDx | Aug 25, 2018 | - - |
Computational 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