chr15-98649674-AAGTG-A
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Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPP3_Moderate
The NM_000875.5(IGF1R):c.94+3_94+6del variant causes a splice donor, splice donor region, coding sequence, intron change. The variant allele was found at a frequency of 0.0000162 in 1,607,578 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
IGF1R
NM_000875.5 splice_donor, splice_donor_region, coding_sequence, intron
NM_000875.5 splice_donor, splice_donor_region, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.72
Genes affected
IGF1R (HGNC:5465): (insulin like growth factor 1 receptor) This receptor binds insulin-like growth factor with a high affinity. It has tyrosine kinase activity. The insulin-like growth factor I receptor plays a critical role in transformation events. Cleavage of the precursor generates alpha and beta subunits. It is highly overexpressed in most malignant tissues where it functions as an anti-apoptotic agent by enhancing cell survival. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.2768031 fraction of the gene. Cryptic splice site detected, with MaxEntScore 6.9, offset of 0 (no position change), new splice context is: aaaGTatgt. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF1R | NM_000875.5 | c.94+3_94+6del | splice_donor_variant, splice_donor_region_variant, coding_sequence_variant, intron_variant | 1/21 | ENST00000650285.1 | ||
IRAIN | NR_126453.2 | n.1110_1113del | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.94+3_94+6del | splice_donor_variant, splice_donor_region_variant, coding_sequence_variant, intron_variant | 1/21 | NM_000875.5 | P4 | |||
IGF1R | ENST00000559925.5 | n.94+3_94+6del | splice_donor_variant, splice_donor_region_variant, non_coding_transcript_exon_variant, intron_variant | 1/10 | 1 | ||||
IGF1R | ENST00000649865.1 | c.94+3_94+6del | splice_donor_variant, splice_donor_region_variant, coding_sequence_variant, intron_variant | 1/21 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151818Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247466Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134388
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GnomAD4 exome AF: 0.0000172 AC: 25AN: 1455760Hom.: 0 AF XY: 0.0000166 AC XY: 12AN XY: 724478
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151818Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74144
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | This sequence change falls in intron 1 of the IGF1R gene. It does not directly change the encoded amino acid sequence of the IGF1R protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs779160550, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with IGF1R-related conditions. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 5
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at