15-98933816-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000875.5(IGF1R):c.2957-1008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,444 control chromosomes in the GnomAD database, including 15,847 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 0.46 ( 15847 hom., cov: 31)
Consequence
IGF1R
NM_000875.5 intron
NM_000875.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.51
Publications
1 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]
IGF1R Gene-Disease associations (from GenCC):
- growth delay due to insulin-like growth factor I resistanceInheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGF1R | ENST00000650285.1 | c.2957-1008G>A | intron_variant | Intron 15 of 20 | NM_000875.5 | ENSP00000497069.1 | ||||
IGF1R | ENST00000560972.1 | n.260-1500G>A | intron_variant | Intron 3 of 3 | 1 | |||||
IGF1R | ENST00000649865.1 | c.2954-1008G>A | intron_variant | Intron 15 of 20 | ENSP00000496919.1 |
Frequencies
GnomAD3 genomes AF: 0.456 AC: 68999AN: 151326Hom.: 15838 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
68999
AN:
151326
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.456 AC: 69049AN: 151444Hom.: 15847 Cov.: 31 AF XY: 0.451 AC XY: 33380AN XY: 73994 show subpopulations
GnomAD4 genome
AF:
AC:
69049
AN:
151444
Hom.:
Cov.:
31
AF XY:
AC XY:
33380
AN XY:
73994
show subpopulations
African (AFR)
AF:
AC:
21529
AN:
41254
American (AMR)
AF:
AC:
6126
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
AC:
1618
AN:
3460
East Asian (EAS)
AF:
AC:
1718
AN:
5124
South Asian (SAS)
AF:
AC:
1524
AN:
4800
European-Finnish (FIN)
AF:
AC:
4356
AN:
10458
Middle Eastern (MID)
AF:
AC:
119
AN:
290
European-Non Finnish (NFE)
AF:
AC:
30774
AN:
67842
Other (OTH)
AF:
AC:
887
AN:
2100
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1872
3744
5615
7487
9359
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
624
1248
1872
2496
3120
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1181
AN:
3478
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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