chr12-75481929-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_006851.3(GLIPR1):c.270C>T(p.His90=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000634 in 1,614,140 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 2 hom. )
Consequence
GLIPR1
NM_006851.3 synonymous
NM_006851.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.108
Genes affected
GLIPR1 (HGNC:17001): (GLI pathogenesis related 1) This gene encodes a protein with similarity to both the pathogenesis-related protein (PR) superfamily and the cysteine-rich secretory protein (CRISP) family. Increased expression of this gene is associated with myelomocytic differentiation in macrophage and decreased expression of this gene through gene methylation is associated with prostate cancer. The protein has proapoptotic activities in prostate and bladder cancer cells. This gene is a member of a cluster on chromosome 12 containing two other similar genes. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 12-75481929-C-T is Benign according to our data. Variant chr12-75481929-C-T is described in ClinVar as [Benign]. Clinvar id is 716437.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.108 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLIPR1 | NM_006851.3 | c.270C>T | p.His90= | synonymous_variant | 2/6 | ENST00000266659.8 | |
GLIPR1 | XM_047428131.1 | c.270C>T | p.His90= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLIPR1 | ENST00000266659.8 | c.270C>T | p.His90= | synonymous_variant | 2/6 | 1 | NM_006851.3 | P1 | |
GLIPR1 | ENST00000456650.7 | c.270C>T | p.His90= | synonymous_variant | 2/6 | 1 | |||
GLIPR1 | ENST00000550491.1 | c.-83C>T | 5_prime_UTR_variant | 2/4 | 3 | ||||
GLIPR1 | ENST00000536703.5 | c.270C>T | p.His90= | synonymous_variant, NMD_transcript_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00343 AC: 522AN: 152148Hom.: 1 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
522
AN:
152148
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.000911 AC: 229AN: 251482Hom.: 0 AF XY: 0.000662 AC XY: 90AN XY: 135914
GnomAD3 exomes
AF:
AC:
229
AN:
251482
Hom.:
AF XY:
AC XY:
90
AN XY:
135914
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000343 AC: 502AN: 1461874Hom.: 2 Cov.: 32 AF XY: 0.000279 AC XY: 203AN XY: 727236
GnomAD4 exome
AF:
AC:
502
AN:
1461874
Hom.:
Cov.:
32
AF XY:
AC XY:
203
AN XY:
727236
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00343 AC: 522AN: 152266Hom.: 1 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74436
GnomAD4 genome
?
AF:
AC:
522
AN:
152266
Hom.:
Cov.:
32
AF XY:
AC XY:
236
AN XY:
74436
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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