chr8-7414857-G-C

Position:

• chr8-7414857-G-C

Variant summary

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

The NM_001205266.2(DEFB4B):​c.*104C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.23 (75 hom., cov: 37)
  • Exomes 𝑓: 0.21 (90 hom.)
  • Failed GnomAD Quality Control
• Consequence: DEFB4B NM_001205266.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

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=-1.02).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEFB4B	NM_001205266.2	c.*104C>G		3_prime_UTR_variant	2/2	ENST00000318157.3	NP_001192195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEFB4B	ENST00000318157.3	c.*104C>G		3_prime_UTR_variant	2/2	1	NM_001205266.2	ENSP00000424598	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 31048 AN: 132694 Hom.: 75 Cov.: 37 FAILED QC

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.221

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.212 AC: 245604 AN: 1158916 Hom.: 90 Cov.: 34 AF XY: 0.213 AC XY: 123343 AN XY: 578392

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.305

Gnomad4 SAS exome AF: 0.225

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.211

Gnomad4 OTH exome AF: 0.223

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.234 AC: 31072 AN: 132800 Hom.: 75 Cov.: 37 AF XY: 0.231 AC XY: 15045 AN XY: 65150

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.222

Alfa AF: 0.146 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2737912; hg19: chr8-7272379; COSMIC: COSV58940067;