Variant NM_030931.4:c.163_166delCAAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_030931.4(DEFB126):c.163_166delCAAA(p.Gln55GlyfsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,613,660 control chromosomes in the GnomAD database, including 20,495 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2602 hom., cov: 28)

Exomes 𝑓: 0.15 ( 17893 hom. )

Consequence

DEFB126
NM_030931.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.332

Variant links:

Genes affected

DEFB126 (HGNC:15900): (defensin beta 126) 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. The encoded protein is highly similar to an epididymal-specific secretory protein (ESP13.2) from cynomolgus monkey. Mutation of this gene is associated with impaired sperm function. [provided by RefSeq, Nov 2014]

DEFB126 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-145514-GCAAA-G is Benign according to our data. Variant chr20-145514-GCAAA-G is described in ClinVar as [Benign]. Clinvar id is 402585.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEFB126	NM_030931.4 link	c.163_166delCAAA	p.Gln55GlyfsTer28	frameshift_variant	Exon 2 of 2	ENST00000382398.4	NP_112193.1	Q9BYW3A0A384MDP8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEFB126	ENST00000382398.4 link	c.163_166delCAAA	p.Gln55GlyfsTer28	frameshift_variant	Exon 2 of 2	1	NM_030931.4	ENSP00000371835.3		Q9BYW3
DEFB126	ENST00000542572.1 link	n.127+31_127+34delCAAA		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27075

AN:

151918

Hom.:

2594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.0712

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.198

GnomAD3 exomes

AF:

0.146

AC:

36734

AN:

251278

Hom.:

3023

AF XY:

0.148

AC XY:

20148

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.264

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.197

Gnomad EAS exome

AF:

0.0632

Gnomad SAS exome

AF:

0.170

Gnomad FIN exome

AF:

0.102

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.153

AC:

223011

AN:

1461624

Hom.:

17893

AF XY:

0.153

AC XY:

111356

AN XY:

727118

show subpopulations

Gnomad4 AFR exome

AF:

0.265

Gnomad4 AMR exome

AF:

0.108

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.0729

Gnomad4 SAS exome

AF:

0.169

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.153

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.178

AC:

27102

AN:

152036

Hom.:

2602

Cov.:

AF XY:

0.174

AC XY:

12925

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.260

Gnomad4 AMR

AF:

0.148

Gnomad4 ASJ

AF:

0.198

Gnomad4 EAS

AF:

0.0716

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.152

Gnomad4 OTH

AF:

0.196

Alfa

AF:

0.168

Hom.:

420

Bravo

AF:

0.185

Asia WGS

AF:

0.140

AC:

487

AN:

3478

EpiCase

AF:

0.163

EpiControl

AF:

0.162

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 2401/12518=19.1% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over