Variant 3-48225345-A-G details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00900

Variant links:

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]

CAMP links:

Genome browser will be placed here

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 linkuse as main transcript	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 linkuse as main transcript	c.434A>G	p.Lys145Arg	missense_variant	4/4		NM_004345.5	A2
CAMP	ENST00000296435.2 linkuse as main transcript	c.443A>G	p.Lys148Arg	missense_variant	4/4	1		P4

Frequencies

GnomAD3 genomes

AF:

0.00225

AC:

343

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000434

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00539

Gnomad FIN

AF:

0.00207

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00335

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00244

AC:

614

AN:

251452

Hom.:

AF XY:

0.00279

AC XY:

379

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00156

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00621

Gnomad FIN exome

AF:

0.00203

Gnomad NFE exome

AF:

0.00275

Gnomad OTH exome

AF:

0.00130

GnomAD4 exome

AF:

0.00264

AC:

3854

AN:

1461102

Hom.:

Cov.:

AF XY:

0.00271

AC XY:

1970

AN XY:

726886

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.00141

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00633

Gnomad4 FIN exome

AF:

0.00199

Gnomad4 NFE exome

AF:

0.00269

Gnomad4 OTH exome

AF:

0.00220

GnomAD4 genome

AF:

0.00226

AC:

344

AN:

152312

Hom.:

Cov.:

AF XY:

0.00228

AC XY:

170

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000433

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00560

Gnomad4 FIN

AF:

0.00207

Gnomad4 NFE

AF:

0.00335

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00258

Hom.:

Bravo

AF:

0.00182

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00130

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00233

AC:

ExAC

AF:

0.00251

AC:

305

Asia WGS

AF:

0.00404

AC:

AN:

3476

EpiCase

AF:

0.00245

EpiControl

AF:

0.00261

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

Cadd

Benign

7.5

Dann

Uncertain

0.98

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.051

LIST_S2

Benign

0.50

M_CAP

Benign

0.0055

MetaRNN

Benign

0.0047

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.34

PROVEAN

Benign

0.020

REVEL

Benign

0.084

Sift

Benign

0.16

Sift4G

Benign

0.19

Vest4

0.15

MVP

0.66

MPC

0.13

ClinPred

0.013

GERP RS

-1.7

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over