chr20-157819-A-G

Variant names:

• chr20-157819-A-G
• rs6077288
• NM_139074.4:c.49+226A>G

Variant summary

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

The NM_139074.4(DEFB127):​c.49+226A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,008 control chromosomes in the GnomAD database, including 7,946 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 0.29 (7946 hom., cov: 32)
• Consequence: DEFB127 NM_139074.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

DEFB127 (HGNC:16206): (defensin beta 127) Defensins are cysteine-rich cationic polypeptides that are important in the immunologic response to invading microorganisms. The antimicrobial protein encoded by this gene is secreted and is a member of the beta defensin protein family. Beta defensin genes are found in several clusters throughout the genome, with this gene mapping to a cluster at 20p13. [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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139074.4. 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
	DEFB127	NM_139074.4	MANE Select	c.49+226A>G		intron	N/A	NP_620713.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB127	ENST00000382388.4	TSL:1 MANE Select	c.49+226A>G		intron	N/A	ENSP00000371825.3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44580 AN: 151890 Hom.: 7950 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.293 AC: 44575 AN: 152008 Hom.: 7946 Cov.: 32 AF XY: 0.300 AC XY: 22291 AN XY: 74314

African (AFR) AF: 0.0888 AC: 3687 AN: 41510

American (AMR) AF: 0.344 AC: 5255 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2675 AN: 5172

South Asian (SAS) AF: 0.444 AC: 2139 AN: 4814

European-Finnish (FIN) AF: 0.418 AC: 4405 AN: 10544

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24139 AN: 67918

Other (OTH) AF: 0.288 AC: 607 AN: 2106

Alfa AF: 0.323 Hom.: 2078

Bravo AF: 0.278

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.54
PhyloP100		-1.1
PromoterAI		0.0062	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6077288; hg19: chr20-138460;