rs951715
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000875.5(IGF1R):c.1828+42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 1,486,490 control chromosomes in the GnomAD database, including 304,719 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 0.64 ( 31317 hom., cov: 34)
Exomes 𝑓: 0.64 ( 273402 hom. )
Consequence
IGF1R
NM_000875.5 intron
NM_000875.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.92
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF1R | NM_000875.5 | c.1828+42G>A | intron_variant | ENST00000650285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.1828+42G>A | intron_variant | NM_000875.5 | P4 | ||||
IGF1R | ENST00000559925.5 | n.1828+42G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
IGF1R | ENST00000649865.1 | c.1828+42G>A | intron_variant | A1 | |||||
IGF1R | ENST00000560144.1 | c.107+42G>A | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.640 AC: 97321AN: 152064Hom.: 31276 Cov.: 34
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GnomAD3 exomes AF: 0.636 AC: 159641AN: 250942Hom.: 51272 AF XY: 0.643 AC XY: 87301AN XY: 135692
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GnomAD4 exome AF: 0.640 AC: 853579AN: 1334306Hom.: 273402 Cov.: 20 AF XY: 0.643 AC XY: 431534AN XY: 670868
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GnomAD4 genome ? AF: 0.640 AC: 97419AN: 152184Hom.: 31317 Cov.: 34 AF XY: 0.640 AC XY: 47611AN XY: 74422
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at