chr8-6876857-C-A

Position:

• chr8-6876857-C-A

Variant summary

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

The NM_005218.4(DEFB1):​c.61+940G>T variant causes a intron 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 0.26 (109 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: DEFB1 NM_005218.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

Genes affected

DEFB1 (HGNC:2766): (defensin beta 1) 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 1, an antimicrobial peptide implicated in the resistance of epithelial surfaces to microbial colonization. This gene maps in close proximity to defensin family member, defensin, alpha 1 and has been implicated in the pathogenesis of cystic fibrosis. [provided by RefSeq, Jul 2008]

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DEFB1	NM_005218.4	c.61+940G>T		intron_variant		ENST00000297439.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEFB1	ENST00000297439.4	c.61+940G>T		intron_variant		1	NM_005218.4	P1
GS1-24F4.2	ENST00000531701.1	n.226-8265C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3806 AN: 14868 Hom.: 108 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.256 AC: 3813 AN: 14872 Hom.: 109 Cov.: 0 AF XY: 0.254 AC XY: 1811 AN XY: 7140

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.090

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

Other links and lift over

dbSNP: rs7003198; hg19: chr8-6734379; COSMIC: COSV52413168;