rs2293960

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005218.4(DEFB1):​c.61+471C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,184 control chromosomes in the GnomAD database, including 50,651 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 0.81 ( 50651 hom., cov: 32)

Consequence

DEFB1
NM_005218.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.74
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DEFB1NM_005218.4 linkuse as main transcriptc.61+471C>G intron_variant ENST00000297439.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DEFB1ENST00000297439.4 linkuse as main transcriptc.61+471C>G intron_variant 1 NM_005218.4 P1
GS1-24F4.2ENST00000531701.1 linkuse as main transcriptn.226-7796G>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.814
AC:
123834
AN:
152066
Hom.:
50612
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.878
Gnomad AMI
AF:
0.723
Gnomad AMR
AF:
0.762
Gnomad ASJ
AF:
0.811
Gnomad EAS
AF:
0.879
Gnomad SAS
AF:
0.848
Gnomad FIN
AF:
0.772
Gnomad MID
AF:
0.892
Gnomad NFE
AF:
0.787
Gnomad OTH
AF:
0.828
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.814
AC:
123935
AN:
152184
Hom.:
50651
Cov.:
32
AF XY:
0.814
AC XY:
60584
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.878
Gnomad4 AMR
AF:
0.762
Gnomad4 ASJ
AF:
0.811
Gnomad4 EAS
AF:
0.879
Gnomad4 SAS
AF:
0.848
Gnomad4 FIN
AF:
0.772
Gnomad4 NFE
AF:
0.787
Gnomad4 OTH
AF:
0.827
Alfa
AF:
0.742
Hom.:
2193
Bravo
AF:
0.815
Asia WGS
AF:
0.827
AC:
2875
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.12
DANN
Benign
0.48

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: rs2293960; hg19: chr8-6734848; API