Genetic Variant LOC124901865:n.7894605T>C (chr8-7894605-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.36 ( 549 hom., cov: 15)

Exomes 𝑓: 0.42 ( 9311 hom. )

Failed GnomAD Quality Control

Consequence

LOC124901865
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

LOC124901865 (HGNC:):

LOC124901865 links:

DEFB4A (HGNC:2767): (defensin beta 4A) Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Members of the defensin family are highly similar in protein sequence. This gene encodes defensin, beta 4, an antibiotic peptide which is locally regulated by inflammation. [provided by RefSeq, Jul 2008]

DEFB4A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901865		n.7894605T>C		intragenic_variant
DEFB4A	NM_004942.4 link	c.-108T>C		upstream_gene_variant		ENST00000302247.3	NP_004933.1	O15263

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEFB4A	ENST00000302247.3 link	c.-108T>C		upstream_gene_variant		1	NM_004942.4	ENSP00000303532.2		O15263

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

35662

AN:

100250

Hom.:

547

Cov.:

FAILED QC

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.401

Gnomad OTH

AF:

0.348

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.417

AC:

432858

AN:

1038982

Hom.:

9311

Cov.:

AF XY:

0.417

AC XY:

218303

AN XY:

524118

show subpopulations

Gnomad4 AFR exome

AF:

0.288

Gnomad4 AMR exome

AF:

0.350

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.464

Gnomad4 SAS exome

AF:

0.412

Gnomad4 FIN exome

AF:

0.417

Gnomad4 NFE exome

AF:

0.423

Gnomad4 OTH exome

AF:

0.408

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.356

AC:

35699

AN:

100356

Hom.:

549

Cov.:

AF XY:

0.357

AC XY:

17225

AN XY:

48264

show subpopulations

Gnomad4 AFR

AF:

0.266

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.382

Gnomad4 EAS

AF:

0.408

Gnomad4 SAS

AF:

0.353

Gnomad4 FIN

AF:

0.405

Gnomad4 NFE

AF:

0.401

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.358

Hom.:

188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.29

DANN

Benign

0.35

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over