chr15-98649653-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000875.5(IGF1R):c.72G>T(p.Ser24Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,988 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
IGF1R
NM_000875.5 synonymous
NM_000875.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.795
Publications
6 publications found
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]
IRAIN (HGNC:50365): (IGF1R antisense imprinted non-protein coding RNA) This gene expresses a long non-coding RNA in antisense to the insulin-like growth factor type I receptor (IGF1R) gene. This transcript is imprinted and expressed from the paternal allele. It interacts with chromatin and may promote long-range DNA interactions that influence the regulation of gene expression. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP7
Synonymous conserved (PhyloP=0.795 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000875.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IGF1R | NM_000875.5 | MANE Select | c.72G>T | p.Ser24Ser | synonymous | Exon 1 of 21 | NP_000866.1 | ||
| IGF1R | NM_001291858.2 | c.72G>T | p.Ser24Ser | synonymous | Exon 1 of 21 | NP_001278787.1 | |||
| IRAIN | NR_126453.2 | n.1135C>A | non_coding_transcript_exon | Exon 1 of 1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IGF1R | ENST00000650285.1 | MANE Select | c.72G>T | p.Ser24Ser | synonymous | Exon 1 of 21 | ENSP00000497069.1 | ||
| IGF1R | ENST00000559925.5 | TSL:1 | n.72G>T | non_coding_transcript_exon | Exon 1 of 10 | ||||
| IGF1R | ENST00000649865.1 | c.72G>T | p.Ser24Ser | synonymous | Exon 1 of 21 | ENSP00000496919.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 246676 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
246676
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457988Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725322 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1457988
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
725322
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33268
American (AMR)
AF:
AC:
0
AN:
44218
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
26068
East Asian (EAS)
AF:
AC:
0
AN:
39486
South Asian (SAS)
AF:
AC:
0
AN:
85708
European-Finnish (FIN)
AF:
AC:
0
AN:
52620
Middle Eastern (MID)
AF:
AC:
0
AN:
5750
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1110624
Other (OTH)
AF:
AC:
0
AN:
60246
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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