rs722829

Positions:

Variant summary

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

The ENST00000334391.5(DEFB128):​c.49+515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,934 control chromosomes in the GnomAD database, including 16,255 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 0.46 ( 16255 hom., cov: 32)

Consequence

DEFB128
ENST00000334391.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.321
Variant links:
Genes affected
DEFB128 (HGNC:18106): (defensin beta 128) Defensins are cysteine-rich cationic polypeptides that are important in the immunologic response to invading microorganisms. The antimicrobial protein encoded by this gene is secreted and is a member of the beta defensin protein family. Beta defensin genes are found in several clusters throughout the genome, with this gene mapping to a cluster at 20p13. [provided by RefSeq, Nov 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DEFB128NM_001037732.3 linkuse as main transcriptc.49+515C>T intron_variant ENST00000334391.5 NP_001032821.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DEFB128ENST00000334391.5 linkuse as main transcriptc.49+515C>T intron_variant 1 NM_001037732.3 ENSP00000335382 P1

Frequencies

GnomAD3 genomes
AF:
0.461
AC:
69967
AN:
151816
Hom.:
16229
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.453
Gnomad AMI
AF:
0.452
Gnomad AMR
AF:
0.487
Gnomad ASJ
AF:
0.470
Gnomad EAS
AF:
0.403
Gnomad SAS
AF:
0.461
Gnomad FIN
AF:
0.465
Gnomad MID
AF:
0.551
Gnomad NFE
AF:
0.462
Gnomad OTH
AF:
0.503
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.461
AC:
70044
AN:
151934
Hom.:
16255
Cov.:
32
AF XY:
0.460
AC XY:
34146
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.453
Gnomad4 AMR
AF:
0.488
Gnomad4 ASJ
AF:
0.470
Gnomad4 EAS
AF:
0.403
Gnomad4 SAS
AF:
0.460
Gnomad4 FIN
AF:
0.465
Gnomad4 NFE
AF:
0.462
Gnomad4 OTH
AF:
0.509
Alfa
AF:
0.464
Hom.:
31730
Bravo
AF:
0.465
Asia WGS
AF:
0.475
AC:
1650
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.90
DANN
Benign
0.52

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: rs722829; hg19: chr20-169701; API