rs2737531

Positions:

• chr8-7414807-C-T

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 0.38 (859 hom., cov: 51)
  • Exomes 𝑓: 0.40 (7909 hom.)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

(HGNC:):

DEFB4B (HGNC:30193): (defensin beta 4B) 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, Oct 2014]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7414807C>T		intergenic_region
DEFB4B	NM_001205266.2	c.*154G>A		downstream_gene_variant		ENST00000318157.3	NP_001192195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEFB4B	ENST00000318157.3	c.*154G>A		downstream_gene_variant		1	NM_001205266.2	ENSP00000424598.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 51988 AN: 137626 Hom.: 860 Cov.: 51 FAILED QC

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.387

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.400 AC: 495114 AN: 1236546 Hom.: 7909 AF XY: 0.401 AC XY: 247011 AN XY: 615674

Gnomad4 AFR exome AF: 0.271

Gnomad4 AMR exome AF: 0.352

Gnomad4 ASJ exome AF: 0.393

Gnomad4 EAS exome AF: 0.455

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.414

Gnomad4 NFE exome AF: 0.404

Gnomad4 OTH exome AF: 0.395

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.378 AC: 52009 AN: 137720 Hom.: 859 Cov.: 51 AF XY: 0.379 AC XY: 25512 AN XY: 67248

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.386

Alfa AF: 0.396 Hom.: 96

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2737531; hg19: chr8-7272329; COSMIC: COSV58940079;