rs2977780

Variant names:

• chr8-6872581-A-G
• rs2977780
• NM_005218.4:c.62-1755T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005218.4(DEFB1):​c.62-1755T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,072 control chromosomes in the GnomAD database, including 2,583 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 0.18 (2583 hom., cov: 32)
• Consequence: DEFB1 NM_005218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.456

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEFB1	NM_005218.4	c.62-1755T>C		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.62-1755T>C		intron_variant	Intron 1 of 1	1	NM_005218.4	ENSP00000297439.3
GS1-24F4.2	ENST00000531701.1	n.226-12541A>G		intron_variant	Intron 2 of 2	3
GS1-24F4.2	ENST00000655804.1	n.323-600A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26829 AN: 151954 Hom.: 2589 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.177 AC: 26845 AN: 152072 Hom.: 2583 Cov.: 32 AF XY: 0.177 AC XY: 13179 AN XY: 74340

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.161

Alfa AF: 0.189 Hom.: 346

Bravo AF: 0.176

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.69

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: rs2977780; hg19: chr8-6730103;