NM_005218.4:c.62-2918delT

Variant names:

• chr8-6873743-GA-G
• rs5743470
• NM_005218.4:c.62-2918delT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DEFB1	NM_005218.4	c.62-2918delT		intron_variant	Intron 1 of 1	ENST00000297439.4	NP_005209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEFB1	ENST00000297439.4	c.62-2918delT		intron_variant	Intron 1 of 1	1	NM_005218.4	ENSP00000297439.3

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

African (AFR) AF: 0.314 AC: 13005 AN: 41408

American (AMR) AF: 0.394 AC: 6012 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1323 AN: 3460

East Asian (EAS) AF: 0.406 AC: 2091 AN: 5152

South Asian (SAS) AF: 0.431 AC: 2074 AN: 4810

European-Finnish (FIN) AF: 0.567 AC: 5978 AN: 10540

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29786 AN: 67844

Other (OTH) AF: 0.401 AC: 842 AN: 2098

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5743470; hg19: chr8-6731265;