rs17847210
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS1
The NM_000875.5(IGF1R):c.570G>A(p.Pro190=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
IGF1R
NM_000875.5 synonymous
NM_000875.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.55
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 15-98708037-G-A is Benign according to our data. Variant chr15-98708037-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2077510.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.55 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000151 (23/152278) while in subpopulation AFR AF= 0.000529 (22/41556). AF 95% confidence interval is 0.000358. There are 0 homozygotes in gnomad4. There are 10 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF1R | NM_000875.5 | c.570G>A | p.Pro190= | synonymous_variant | 2/21 | ENST00000650285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.570G>A | p.Pro190= | synonymous_variant | 2/21 | NM_000875.5 | P4 | ||
IGF1R | ENST00000559925.5 | n.570G>A | non_coding_transcript_exon_variant | 2/10 | 1 | ||||
IGF1R | ENST00000649865.1 | c.570G>A | p.Pro190= | synonymous_variant | 2/21 | A1 | |||
IGF1R | ENST00000558355.1 | c.207G>A | p.Pro69= | synonymous_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000639 AC: 16AN: 250544Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135448
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461800Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727204
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GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74464
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
Computational 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