20-31418506-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

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
DEFB121	XM_005260383.3	c.-416G>A		5_prime_UTR_variant	Exon 1 of 4		XP_005260440.1

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

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

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

Other links and lift over

dbSNP: rs721220; hg19: chr20-30006309;