rs6059244

Variant names:

• chr20-31422680-A-G
• rs6059244
• ENST00000433453.1:n.257-1002T>C

Variant summary

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

The ENST00000433453.1(DEFB122):​n.257-1002T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,972 control chromosomes in the GnomAD database, including 28,798 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 0.61 (28798 hom., cov: 32)
• Consequence: DEFB122 ENST00000433453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 11 publications found

Genes affected

DEFB122 (HGNC:):

DEFB122 (HGNC:18102): (defensin beta 122 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433453.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB122	NR_045677.1		n.257-1002T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB122	ENST00000433453.1	TSL:1	n.257-1002T>C		intron	N/A
	DEFB122	ENST00000569013.1	TSL:6	n.49-1002T>C		intron	N/A
	DEFB122	ENST00000722580.1		n.202-1002T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92897 AN: 151854 Hom.: 28770 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.616

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.612 AC: 92958 AN: 151972 Hom.: 28798 Cov.: 32 AF XY: 0.611 AC XY: 45377 AN XY: 74270

African (AFR) AF: 0.530 AC: 21947 AN: 41440

American (AMR) AF: 0.636 AC: 9706 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3837 AN: 5176

South Asian (SAS) AF: 0.732 AC: 3532 AN: 4824

European-Finnish (FIN) AF: 0.579 AC: 6091 AN: 10516

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43366 AN: 67966

Other (OTH) AF: 0.614 AC: 1294 AN: 2108

Alfa AF: 0.636 Hom.: 16432

Bravo AF: 0.610

Asia WGS AF: 0.714 AC: 2484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6059244; hg19: chr20-30010483;