ENST00000296435.2:c.-271G>A

Variant names:

• chr3-48223232-G-A
• rs9844812
• ENST00000296435.2:c.-271G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000296435.2(CAMP):​c.-271G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 503,790 control chromosomes in the GnomAD database, including 571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.042 (453 hom., cov: 32)
  • Exomes 𝑓: 0.0066 (118 hom.)
• Consequence: CAMP ENST00000296435.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMP	ENST00000296435.2	c.-271G>A		upstream_gene_variant		1		ENSP00000296435.2

Frequencies

GnomAD3 genomes AF: 0.0422 AC: 6419 AN: 152122 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0199

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000620

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.0302

GnomAD4 exome AF: 0.00656 AC: 2307 AN: 351550 Hom.: 118 AF XY: 0.00564 AC XY: 1034 AN XY: 183434

African (AFR) AF: 0.141 AC: 1473 AN: 10420

American (AMR) AF: 0.0148 AC: 191 AN: 12872

Ashkenazi Jewish (ASJ) AF: 0.00613 AC: 69 AN: 11254

East Asian (EAS) AF: 0.00 AC: 0 AN: 23302

South Asian (SAS) AF: 0.000366 AC: 13 AN: 35478

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23326

Middle Eastern (MID) AF: 0.0106 AC: 17 AN: 1608

European-Non Finnish (NFE) AF: 0.00117 AC: 248 AN: 212394

Other (OTH) AF: 0.0142 AC: 296 AN: 20896

GnomAD4 genome AF: 0.0422 AC: 6426 AN: 152240 Hom.: 453 Cov.: 32 AF XY: 0.0408 AC XY: 3034 AN XY: 74438

African (AFR) AF: 0.143 AC: 5953 AN: 41508

American (AMR) AF: 0.0197 AC: 302 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00121 AC: 82 AN: 68020

Other (OTH) AF: 0.0299 AC: 63 AN: 2110

Alfa AF: 0.0184 Hom.: 186

Bravo AF: 0.0484

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		-1.7
PromoterAI		-0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9844812; hg19: chr3-48264722;