3-46551578-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024512.5(LRRC2):āc.14T>Cā(p.Val5Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000417 in 1,612,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00046 ( 0 hom., cov: 33)
Exomes š: 0.00041 ( 0 hom. )
Consequence
LRRC2
NM_024512.5 missense
NM_024512.5 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 5.86
Genes affected
LRRC2 (HGNC:14676): (leucine rich repeat containing 2) This gene encodes a member of the leucine-rich repeat-containing family of proteins, which function in diverse biological pathways. This family member may possibly be a nuclear protein. Similarity to the RAS suppressor protein, as well as expression down-regulation observed in tumor cells, suggests that it may function as a tumor suppressor. The gene is located in the chromosome 3 common eliminated region 1 (C3CER1), a 1.4 Mb region that is commonly deleted in diverse tumors. A related pseudogene has been identified on chromosome 2. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.21796235).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC2 | NM_024512.5 | c.14T>C | p.Val5Ala | missense_variant | 2/9 | ENST00000395905.8 | NP_078788.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC2 | ENST00000395905.8 | c.14T>C | p.Val5Ala | missense_variant | 2/9 | 1 | NM_024512.5 | ENSP00000379241 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000479 AC: 120AN: 250340Hom.: 0 AF XY: 0.000540 AC XY: 73AN XY: 135228
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GnomAD4 exome AF: 0.000413 AC: 603AN: 1460798Hom.: 0 Cov.: 31 AF XY: 0.000425 AC XY: 309AN XY: 726592
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GnomAD4 genome AF: 0.000460 AC: 70AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.000363 AC XY: 27AN XY: 74340
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | The c.14T>C (p.V5A) alteration is located in exon 2 (coding exon 1) of the LRRC2 gene. This alteration results from a T to C substitution at nucleotide position 14, causing the valine (V) at amino acid position 5 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
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