chr12-75481887-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_006851.3(GLIPR1):c.228G>A(p.Gln76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000635 in 1,614,120 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: -1.54
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 12-75481887-G-A is Benign according to our data. Variant chr12-75481887-G-A is described in ClinVar as [Benign]. Clinvar id is 716436.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLIPR1 | NM_006851.3 | c.228G>A | p.Gln76= | synonymous_variant | 2/6 | ENST00000266659.8 | |
GLIPR1 | XM_047428131.1 | c.228G>A | p.Gln76= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLIPR1 | ENST00000266659.8 | c.228G>A | p.Gln76= | synonymous_variant | 2/6 | 1 | NM_006851.3 | P1 | |
GLIPR1 | ENST00000456650.7 | c.228G>A | p.Gln76= | synonymous_variant | 2/6 | 1 | |||
GLIPR1 | ENST00000550491.1 | c.-125G>A | 5_prime_UTR_variant | 2/4 | 3 | ||||
GLIPR1 | ENST00000536703.5 | c.228G>A | p.Gln76= | synonymous_variant, NMD_transcript_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00344 AC: 523AN: 152152Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000911 AC: 229AN: 251356Hom.: 0 AF XY: 0.000662 AC XY: 90AN XY: 135854
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GnomAD4 exome AF: 0.000343 AC: 502AN: 1461850Hom.: 2 Cov.: 32 AF XY: 0.000279 AC XY: 203AN XY: 727226
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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
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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