20-31418506-C-T

Variant summary

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

The XM_005260383.3(DEFB121):​c.-416G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,818 control chromosomes in the GnomAD database, including 16,819 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 0.43 ( 16819 hom., cov: 31)

Consequence

DEFB121
XM_005260383.3 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.193
Variant links:
Genes affected
DEFB121 (HGNC:18101): (defensin beta 121) This gene encodes a member of the beta subfamily of defensins. Beta-defensins are antimicrobial peptides that protect tissues and organs from infection by a variety of microorganisms. This gene is found in a cluster with other beta-defensin genes on the long arm of chromosome 20. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2014]

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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=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DEFB121XM_005260383.3 linkc.-416G>A 5_prime_UTR_variant Exon 1 of 4 XP_005260440.1 Q5GRF9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.434
AC:
65813
AN:
151700
Hom.:
16812
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.651
Gnomad AMR
AF:
0.542
Gnomad ASJ
AF:
0.488
Gnomad EAS
AF:
0.739
Gnomad SAS
AF:
0.660
Gnomad FIN
AF:
0.506
Gnomad MID
AF:
0.538
Gnomad NFE
AF:
0.525
Gnomad OTH
AF:
0.443
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.434
AC:
65816
AN:
151818
Hom.:
16819
Cov.:
31
AF XY:
0.439
AC XY:
32577
AN XY:
74142
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.542
Gnomad4 ASJ
AF:
0.488
Gnomad4 EAS
AF:
0.739
Gnomad4 SAS
AF:
0.661
Gnomad4 FIN
AF:
0.506
Gnomad4 NFE
AF:
0.525
Gnomad4 OTH
AF:
0.443
Alfa
AF:
0.459
Hom.:
2152
Bravo
AF:
0.422
Asia WGS
AF:
0.651
AC:
2265
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
6.3
DANN
Benign
0.73

Splicing

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: rs721220; hg19: chr20-30006309; API