8-6873758-C-T

Variant names:

• chr8-6873758-C-T
• rs2741126
• NM_005218.4:c.62-2932G>A

Variant summary

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

The NM_005218.4(DEFB1):​c.62-2932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,778 control chromosomes in the GnomAD database, including 19,560 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 0.50 (19560 hom., cov: 31)
• Consequence: DEFB1 NM_005218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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.62-2932G>A		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.62-2932G>A		intron	N/A	ENSP00000297439.3	P60022
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-11364C>T		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-11364C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76274 AN: 151662 Hom.: 19549 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.503 AC: 76329 AN: 151778 Hom.: 19560 Cov.: 31 AF XY: 0.505 AC XY: 37452 AN XY: 74166

African (AFR) AF: 0.605 AC: 25034 AN: 41394

American (AMR) AF: 0.444 AC: 6777 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3460

East Asian (EAS) AF: 0.439 AC: 2264 AN: 5156

South Asian (SAS) AF: 0.456 AC: 2194 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6078 AN: 10532

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31139 AN: 67858

Other (OTH) AF: 0.474 AC: 1000 AN: 2108

Alfa AF: 0.465 Hom.: 21087

Bravo AF: 0.498

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.53
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2741126; hg19: chr8-6731280;