20-31418506-C-T

Variant names:

• chr20-31418506-C-T
• rs721220
• XM_005260383.3:c.-416G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65813 AN: 151700 Hom.: 16812 Cov.: 31

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

African (AFR) AF: 0.151 AC: 6260 AN: 41450

American (AMR) AF: 0.542 AC: 8275 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3468

East Asian (EAS) AF: 0.739 AC: 3788 AN: 5128

South Asian (SAS) AF: 0.661 AC: 3166 AN: 4788

European-Finnish (FIN) AF: 0.506 AC: 5313 AN: 10504

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35639 AN: 67908

Other (OTH) AF: 0.443 AC: 935 AN: 2110

Alfa AF: 0.448 Hom.: 2168

Bravo AF: 0.422

Asia WGS AF: 0.651 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.3
DANN	Benign	0.73
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs721220; hg19: chr20-30006309;