rs5743439

Variant names:

• chr8-6876278-C-A
• rs5743439
• NM_005218.4:c.61+1519G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-6876278-C-A
• chr8-6876278-C-G
• chr8-6876278-C-T

Variant summary

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

The NM_005218.4(DEFB1):​c.61+1519G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,024 control chromosomes in the GnomAD database, including 51,677 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 0.82 (51677 hom., cov: 31)
• Consequence: DEFB1 NM_005218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005218.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB1	NM_005218.4	MANE Select	c.61+1519G>T		intron	N/A	NP_005209.1	P60022

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB1	ENST00000297439.4	TSL:1 MANE Select	c.61+1519G>T		intron	N/A	ENSP00000297439.3	P60022
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-8844C>A		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-8844C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.823 AC: 124982 AN: 151906 Hom.: 51636 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.823 AC: 125088 AN: 152024 Hom.: 51677 Cov.: 31 AF XY: 0.822 AC XY: 61074 AN XY: 74300

African (AFR) AF: 0.889 AC: 36838 AN: 41450

American (AMR) AF: 0.764 AC: 11667 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3470

East Asian (EAS) AF: 0.883 AC: 4556 AN: 5160

South Asian (SAS) AF: 0.853 AC: 4109 AN: 4818

European-Finnish (FIN) AF: 0.778 AC: 8209 AN: 10552

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54195 AN: 67984

Other (OTH) AF: 0.835 AC: 1764 AN: 2112

Alfa AF: 0.810 Hom.: 6213

Bravo AF: 0.824

Asia WGS AF: 0.826 AC: 2871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.64
PhyloP100		-0.95
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: rs5743439; hg19: chr8-6733800;