rs6059244

chr20-31422680-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_045677.1(DEFB122):n.257-1002T>C variant causes a intron, non coding transcript 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 NR_045677.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DEFB122	NR_045677.1	n.257-1002T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEFB122	ENST00000433453.1	n.257-1002T>C		intron_variant, non_coding_transcript_variant		1
DEFB122	ENST00000569013.1	n.49-1002T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.614

Alfa AF: 0.636 Hom.: 14711

Bravo AF: 0.610

Asia WGS AF: 0.714 AC: 2484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6059244; hg19: chr20-30010483;