chr7-29146736-T-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001398427.1(CHN2):c.-511T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00076 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CHN2
NM_001398427.1 5_prime_UTR
NM_001398427.1 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.82
Genes affected
CHN2 (HGNC:1944): (chimerin 2) This gene encodes a guanosine triphosphate (GTP)-metabolizing protein that contains a phorbol-ester/diacylglycerol (DAG)-type zinc finger, a Rho-GAP domain, and an SH2 domain. The encoded protein translocates from the cytosol to the Golgi apparatus membrane upon binding by diacylglycerol (DAG). Activity of this protein is important in cell proliferation and migration, and expression changes in this gene have been detected in cancers. A mutation in this gene has also been associated with schizophrenia in men. Alternative transcript splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, May 2014]
CPVL (HGNC:14399): (carboxypeptidase vitellogenic like) The protein encoded by this gene is a carboxypeptidase and bears strong sequence similarity to serine carboxypeptidases. Carboxypeptidases are a large class of proteases that act to cleave a single amino acid from the carboxy termini of proteins or peptides. The exact function of this protein, however, has not been determined. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 7-29146736-T-G is Benign according to our data. Variant chr7-29146736-T-G is described in ClinVar as [Benign]. Clinvar id is 3035343.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHN2 | NM_001398427.1 | c.-511T>G | 5_prime_UTR_variant | 1/14 | NP_001385356.1 | |||
CHN2 | XM_011515105.3 | c.-589T>G | 5_prime_UTR_variant | 1/16 | XP_011513407.2 | |||
CHN2 | XM_011515106.3 | c.-550T>G | 5_prime_UTR_variant | 1/15 | XP_011513408.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPVL | ENST00000409850.5 | c.-10-25665A>C | intron_variant | 2 | ENSP00000387164 | P1 | ||||
CPVL | ENST00000437527.1 | c.-10-25665A>C | intron_variant | 4 | ENSP00000416555 | |||||
CPVL | ENST00000449801.5 | c.-10-25665A>C | intron_variant | 4 | ENSP00000413287 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 4AN: 151846Hom.: 0 Cov.: 33 FAILED QC
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GnomAD3 exomes AF: 0.00326 AC: 481AN: 147412Hom.: 0 AF XY: 0.00275 AC XY: 218AN XY: 79366
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000755 AC: 1050AN: 1390368Hom.: 0 Cov.: 59 AF XY: 0.000698 AC XY: 479AN XY: 685870
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000263 AC: 4AN: 151846Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74150
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CHN2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at