NM_001567.4:c.45C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001567.4(INPPL1):c.45C>T(p.Gly15Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
INPPL1
NM_001567.4 synonymous
NM_001567.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.194
Publications
0 publications found
Genes affected
INPPL1 (HGNC:6080): (inositol polyphosphate phosphatase like 1) The protein encoded by this gene is an SH2-containing 5'-inositol phosphatase that is involved in the regulation of insulin function. The encoded protein also plays a role in the regulation of epidermal growth factor receptor turnover and actin remodelling. Additionally, this gene supports metastatic growth in breast cancer and is a valuable biomarker for breast cancer. [provided by RefSeq, Jan 2009]
INPPL1 Gene-Disease associations (from GenCC):
- opsismodysplasiaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
- schneckenbecken dysplasiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 11-72225029-C-T is Benign according to our data. Variant chr11-72225029-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1643960.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.194 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001567.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INPPL1 | NM_001567.4 | MANE Select | c.45C>T | p.Gly15Gly | synonymous | Exon 1 of 28 | NP_001558.3 | ||
| INPPL1 | NM_001440434.1 | c.45C>T | p.Gly15Gly | synonymous | Exon 1 of 28 | NP_001427363.1 | |||
| INPPL1 | NM_001440435.1 | c.45C>T | p.Gly15Gly | synonymous | Exon 2 of 29 | NP_001427364.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INPPL1 | ENST00000298229.7 | TSL:1 MANE Select | c.45C>T | p.Gly15Gly | synonymous | Exon 1 of 28 | ENSP00000298229.2 | O15357-1 | |
| INPPL1 | ENST00000924957.1 | c.45C>T | p.Gly15Gly | synonymous | Exon 2 of 29 | ENSP00000595016.1 | |||
| INPPL1 | ENST00000946902.1 | c.45C>T | p.Gly15Gly | synonymous | Exon 2 of 29 | ENSP00000616961.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1071998Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 506780
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1071998
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
506780
African (AFR)
AF:
AC:
0
AN:
22486
American (AMR)
AF:
AC:
0
AN:
8052
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
13856
East Asian (EAS)
AF:
AC:
0
AN:
25892
South Asian (SAS)
AF:
AC:
0
AN:
19614
European-Finnish (FIN)
AF:
AC:
0
AN:
20978
Middle Eastern (MID)
AF:
AC:
0
AN:
2886
European-Non Finnish (NFE)
AF:
AC:
0
AN:
915326
Other (OTH)
AF:
AC:
0
AN:
42908
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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