rs7003198

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

2

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]

Genome browser will be placed here

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
DEFB1NM_005218.4 linkuse as main transcriptc.61+940G>T intron_variant ENST00000297439.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DEFB1ENST00000297439.4 linkuse as main transcriptc.61+940G>T intron_variant 1 NM_005218.4 P1
GS1-24F4.2ENST00000531701.1 linkuse as main transcriptn.226-8265C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
3806
AN:
14868
Hom.:
108
Cov.:
0
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.:
0
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.

Other links and lift over

dbSNP: rs7003198; hg19: chr8-6734379; COSMIC: COSV52413168; API