Variant rs2740091 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001205266.2(DEFB4B):c.*44C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.21 ( 33 hom., cov: 30)

Exomes 𝑓: 0.20 ( 29 hom. )

Failed GnomAD Quality Control

Consequence

DEFB4B
NM_001205266.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301

Variant links:

Genes affected

DEFB4B (HGNC:30193): (defensin beta 4B) 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 4, an antibiotic peptide which is locally regulated by inflammation. [provided by RefSeq, Oct 2014]

DEFB4B links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEFB4B	NM_001205266.2 link	c.*44C>T		3_prime_UTR_variant	2/2	ENST00000318157.3	NP_001192195.1	O15263

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEFB4B	ENST00000318157 link	c.*44C>T		3_prime_UTR_variant	2/2	1	NM_001205266.2	ENSP00000424598.1		O15263

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

27358

AN:

131268

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.312

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.183

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.205

GnomAD3 exomes

AF:

0.214

AC:

16325

AN:

76442

Hom.:

AF XY:

0.216

AC XY:

8193

AN XY:

37890

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.136

Gnomad ASJ exome

AF:

0.244

Gnomad EAS exome

AF:

0.310

Gnomad SAS exome

AF:

0.231

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.226

Gnomad OTH exome

AF:

0.228

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.203

AC:

161857

AN:

798372

Hom.:

Cov.:

AF XY:

0.205

AC XY:

83185

AN XY:

404816

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.304

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.199

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.208

AC:

27373

AN:

131350

Hom.:

Cov.:

AF XY:

0.206

AC XY:

13229

AN XY:

64260

show subpopulations

Gnomad4 AFR

AF:

0.163

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.313

Gnomad4 SAS

AF:

0.216

Gnomad4 FIN

AF:

0.208

Gnomad4 NFE

AF:

0.240

Gnomad4 OTH

AF:

0.206

Alfa

AF:

0.152

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.6

DANN

Benign

0.84

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over