chr3-48225345-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004345.5(CAMP):c.434A>G(p.Lys145Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,613,414 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0026 ( 15 hom. )
Consequence
CAMP
NM_004345.5 missense
NM_004345.5 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 0.00900
Genes affected
CAMP (HGNC:1472): (cathelicidin antimicrobial peptide) This gene encodes a member of an antimicrobial peptide family, characterized by a highly conserved N-terminal signal peptide containing a cathelin domain and a structurally variable cationic antimicrobial peptide, which is produced by extracellular proteolysis from the C-terminus. The protein plays an important role in innate immunity defense against viruses. In addition to its antibacterial, antifungal, and antiviral activities, the encoded protein functions in cell chemotaxis, immune mediator induction, and inflammatory response regulation. [provided by RefSeq, Sep 2021]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004702896).
BP6
?
Variant 3-48225345-A-G is Benign according to our data. Variant chr3-48225345-A-G is described in ClinVar as [Benign]. Clinvar id is 733963.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMP | NM_004345.5 | c.434A>G | p.Lys145Arg | missense_variant | 4/4 | ENST00000652295.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMP | ENST00000652295.2 | c.434A>G | p.Lys145Arg | missense_variant | 4/4 | NM_004345.5 | A2 | ||
CAMP | ENST00000296435.2 | c.443A>G | p.Lys148Arg | missense_variant | 4/4 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00225 AC: 343AN: 152194Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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152194
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GnomAD3 exomes AF: 0.00244 AC: 614AN: 251452Hom.: 3 AF XY: 0.00279 AC XY: 379AN XY: 135912
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GnomAD4 exome AF: 0.00264 AC: 3854AN: 1461102Hom.: 15 Cov.: 30 AF XY: 0.00271 AC XY: 1970AN XY: 726886
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GnomAD4 genome ? AF: 0.00226 AC: 344AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.00228 AC XY: 170AN XY: 74482
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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 | Aug 14, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
GERP RS
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