chr4-17522947-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001079827.2(CLRN2):c.337C>G(p.Leu113Val) variant causes a missense change. The variant allele was found at a frequency of 0.129 in 1,613,840 control chromosomes in the GnomAD database, including 14,301 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.10 ( 966 hom., cov: 33)
Exomes 𝑓: 0.13 ( 13335 hom. )
Consequence
CLRN2
NM_001079827.2 missense
NM_001079827.2 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 3.97
Genes affected
CLRN2 (HGNC:33939): (clarin 2) This gene belongs to the clarin family of genes. The clarins appear to belong to a large superfamily of small integral membrane glycoproteins with four transmembrane domains. The exact function of this gene is unknown. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0018548369).
BP6
?
Variant 4-17522947-C-G is Benign according to our data. Variant chr4-17522947-C-G is described in ClinVar as [Benign]. Clinvar id is 1286756.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLRN2 | NM_001079827.2 | c.337C>G | p.Leu113Val | missense_variant | 2/3 | ENST00000511148.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLRN2 | ENST00000511148.2 | c.337C>G | p.Leu113Val | missense_variant | 2/3 | 1 | NM_001079827.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.103 AC: 15687AN: 152140Hom.: 962 Cov.: 33
GnomAD3 genomes
?
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33
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GnomAD3 exomes AF: 0.130 AC: 32385AN: 249170Hom.: 2322 AF XY: 0.131 AC XY: 17760AN XY: 135162
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GnomAD4 exome AF: 0.132 AC: 192340AN: 1461582Hom.: 13335 Cov.: 32 AF XY: 0.132 AC XY: 96225AN XY: 727064
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GnomAD4 genome ? AF: 0.103 AC: 15699AN: 152258Hom.: 966 Cov.: 33 AF XY: 0.104 AC XY: 7707AN XY: 74444
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474
ESP6500AA
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127
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1141
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?
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15497
Asia WGS
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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 | GeneDx | Apr 27, 2020 | This variant is associated with the following publications: (PMID: 31448880) - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
M
MutationTaster
Benign
P
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at