Variant 3-48224434-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004345.5(CAMP):c.282A>G(p.Pro94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,613,458 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0011 ( 6 hom. )

Consequence

CAMP
NM_004345.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.34

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 3-48224434-A-G is Benign according to our data. Variant chr3-48224434-A-G is described in ClinVar as [Benign]. Clinvar id is 708654.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4.34 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMP	NM_004345.5 linkuse as main transcript	c.282A>G	p.Pro94=	synonymous_variant	2/4	ENST00000652295.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMP	ENST00000652295.2 linkuse as main transcript	c.282A>G	p.Pro94=	synonymous_variant	2/4		NM_004345.5	A2
CAMP	ENST00000296435.2 linkuse as main transcript	c.291A>G	p.Pro97=	synonymous_variant	2/4	1		P4

Frequencies

GnomAD3 genomes

AF:

0.00319

AC:

485

AN:

152116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00758

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.0184

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000529

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00183

AC:

460

AN:

251162

Hom.:

AF XY:

0.00157

AC XY:

213

AN XY:

135776

show subpopulations

Gnomad AFR exome

AF:

0.00813

Gnomad AMR exome

AF:

0.00133

Gnomad ASJ exome

AF:

0.0188

Gnomad EAS exome

AF:

0.000870

Gnomad SAS exome

AF:

0.000229

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000502

Gnomad OTH exome

AF:

0.00212

GnomAD4 exome

AF:

0.00105

AC:

1538

AN:

1461224

Hom.:

Cov.:

AF XY:

0.00102

AC XY:

744

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.00908

Gnomad4 AMR exome

AF:

0.00145

Gnomad4 ASJ exome

AF:

0.0162

Gnomad4 EAS exome

AF:

0.00378

Gnomad4 SAS exome

AF:

0.000325

Gnomad4 FIN exome

AF:

0.0000375

Gnomad4 NFE exome

AF:

0.000353

Gnomad4 OTH exome

AF:

0.00267

GnomAD4 genome

AF:

0.00325

AC:

494

AN:

152234

Hom.:

Cov.:

AF XY:

0.00328

AC XY:

244

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00777

Gnomad4 AMR

AF:

0.00347

Gnomad4 ASJ

AF:

0.0184

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000529

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00262

Hom.:

Bravo

AF:

0.00368

Asia WGS

AF:

0.00577

AC:

AN:

3478

EpiCase

AF:

0.000981

EpiControl

AF:

0.000948

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

Apr 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.044

DANN

Benign

0.37

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