Variant rs7003198 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_005218.4(DEFB1):c.61+940G>T variant causes a intron 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 0.26 ( 109 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

DEFB1
NM_005218.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Variant links:

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]

DEFB1 links:

GS1-24F4.2 (HGNC:):

GS1-24F4.2 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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DEFB1	NM_005218.4 linkuse as main transcript	c.61+940G>T		intron_variant		ENST00000297439.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEFB1	ENST00000297439.4 linkuse as main transcript	c.61+940G>T		intron_variant		1	NM_005218.4	P1
GS1-24F4.2	ENST00000531701.1 linkuse as main transcript	n.226-8265C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

3806

AN:

14868

Hom.:

108

Cov.:

FAILED QC

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.400

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

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

AF:

0.256

AC:

3813

AN:

14872

Hom.:

109

Cov.:

AF XY:

0.254

AC XY:

1811

AN XY:

7140

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.349

Gnomad4 SAS

AF:

0.280

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.3

DANN

Benign

0.090

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