15-98960461-A-AT
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000875.5(IGF1R):c.*3020dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 233,010 control chromosomes in the GnomAD database, including 5,056 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3379 hom., cov: 28)
Exomes 𝑓: 0.19 ( 1677 hom. )
Consequence
IGF1R
NM_000875.5 3_prime_UTR
NM_000875.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.669
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 Benign. Variant got -10 ACMG points.
BP6
Variant 15-98960461-A-AT is Benign according to our data. Variant chr15-98960461-A-AT is described in ClinVar as [Likely_benign]. Clinvar id is 317544.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF1R | NM_000875.5 | c.*3020dup | 3_prime_UTR_variant | 21/21 | ENST00000650285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.*3020dup | 3_prime_UTR_variant | 21/21 | NM_000875.5 | P4 | |||
SYNM-AS1 | ENST00000559468.1 | n.348+5527_348+5528insA | intron_variant, non_coding_transcript_variant | 4 | |||||
IGF1R | ENST00000649865.1 | c.*3020dup | 3_prime_UTR_variant | 21/21 | A1 |
Frequencies
GnomAD3 genomes AF: 0.205 AC: 31141AN: 152002Hom.: 3375 Cov.: 28
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GnomAD4 exome AF: 0.192 AC: 15510AN: 80890Hom.: 1677 Cov.: 0 AF XY: 0.191 AC XY: 7108AN XY: 37182
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GnomAD4 genome AF: 0.205 AC: 31157AN: 152120Hom.: 3379 Cov.: 28 AF XY: 0.200 AC XY: 14871AN XY: 74366
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Growth delay due to insulin-like growth factor I resistance Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at