rs5743470

Positions:

• chr8-6873743-GA-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_005218.4(DEFB1):​c.62-2918delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (12808 hom., cov: 0)
• Consequence: DEFB1 NM_005218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

Genes affected

DEFB1 (HGNC:2766): (defensin beta 1) Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Members of the defensin family are highly similar in protein sequence. This gene encodes defensin, beta 1, an antimicrobial peptide implicated in the resistance of epithelial surfaces to microbial colonization. This gene maps in close proximity to defensin family member, defensin, alpha 1 and has been implicated in the pathogenesis of cystic fibrosis. [provided by RefSeq, Jul 2008]

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEFB1	NM_005218.4	c.62-2918delT		intron_variant		ENST00000297439.4	NP_005209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEFB1	ENST00000297439.4	c.62-2918delT		intron_variant		1	NM_005218.4	ENSP00000297439.3
GS1-24F4.2	ENST00000531701.1	n.226-11378delA		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61558 AN: 151654 Hom.: 12806 Cov.: 0

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 61566 AN: 151770 Hom.: 12808 Cov.: 0 AF XY: 0.410 AC XY: 30415 AN XY: 74156

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.401

Alfa AF: 0.259 Hom.: 558

Bravo AF: 0.390

Asia WGS AF: 0.359 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs5743470; hg19: chr8-6731265;