Variant 20-145669-ACC-A 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.317_318delCC(p.Pro106ArgfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,611,132 control chromosomes in the GnomAD database, including 252,198 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 23238 hom., cov: 0)

Exomes 𝑓: 0.56 ( 228960 hom. )

Consequence

DEFB126
NM_030931.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.249

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-145669-ACC-A is Benign according to our data. Variant chr20-145669-ACC-A is described in ClinVar as [Benign]. Clinvar id is 402586.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEFB126	NM_030931.4 link	c.317_318delCC	p.Pro106ArgfsTer26	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.317_318delCC	p.Pro106ArgfsTer26	frameshift_variant	Exon 2 of 2	1	NM_030931.4	ENSP00000371835.3		Q9BYW3
DEFB126	ENST00000542572.1 link	n.222_223delCC		non_coding_transcript_exon_variant	Exon 3 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.552

AC:

83680

AN:

151478

Hom.:

23225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.639

Gnomad AMR

AF:

0.547

Gnomad ASJ

AF:

0.689

Gnomad EAS

AF:

0.505

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.567

GnomAD3 exomes

AF:

0.552

AC:

137216

AN:

248480

Hom.:

38189

AF XY:

0.558

AC XY:

75034

AN XY:

134538

show subpopulations

Gnomad AFR exome

AF:

0.552

Gnomad AMR exome

AF:

0.519

Gnomad ASJ exome

AF:

0.685

Gnomad EAS exome

AF:

0.508

Gnomad SAS exome

AF:

0.593

Gnomad FIN exome

AF:

0.493

Gnomad NFE exome

AF:

0.557

Gnomad OTH exome

AF:

0.566

GnomAD4 exome

AF:

0.559

AC:

815255

AN:

1459534

Hom.:

228960

AF XY:

0.561

AC XY:

407148

AN XY:

726052

show subpopulations

Gnomad4 AFR exome

AF:

0.554

Gnomad4 AMR exome

AF:

0.526

Gnomad4 ASJ exome

AF:

0.688

Gnomad4 EAS exome

AF:

0.506

Gnomad4 SAS exome

AF:

0.596

Gnomad4 FIN exome

AF:

0.485

Gnomad4 NFE exome

AF:

0.559

Gnomad4 OTH exome

AF:

0.568

GnomAD4 genome

AF:

0.552

AC:

83732

AN:

151598

Hom.:

23238

Cov.:

AF XY:

0.549

AC XY:

40663

AN XY:

74072

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.546

Gnomad4 ASJ

AF:

0.689

Gnomad4 EAS

AF:

0.505

Gnomad4 SAS

AF:

0.598

Gnomad4 FIN

AF:

0.488

Gnomad4 NFE

AF:

0.556

Gnomad4 OTH

AF:

0.560

Alfa

AF:

0.567

Hom.:

4505

Bravo

AF:

0.559

Asia WGS

AF:

0.491

AC:

1711

AN:

3478

EpiCase

AF:

0.574

EpiControl

AF:

0.571

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): 7088/12518=56.6% -

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