chr8-7894605-T-C

Variant names:

• chr8-7894605-T-C
• rs2740086

Variant summary

Our verdict is Likely benign. The variant received -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

Genes affected

LOC124901865 (HGNC:):

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000302247.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB4A	NM_004942.4	MANE Select	c.-108T>C		upstream_gene	N/A	NP_004933.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEFB4A	ENST00000302247.3	TSL:1 MANE Select	c.-108T>C		upstream_gene	N/A	ENSP00000303532.2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 35662 AN: 100250 Hom.: 547 Cov.: 15

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.: 16 AF XY: 0.417 AC XY: 218303 AN XY: 524118

African (AFR) AF: 0.288 AC: 6896 AN: 23982

American (AMR) AF: 0.350 AC: 10971 AN: 31376

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 7745 AN: 18934

East Asian (EAS) AF: 0.464 AC: 15469 AN: 33354

South Asian (SAS) AF: 0.412 AC: 27050 AN: 65676

European-Finnish (FIN) AF: 0.417 AC: 17921 AN: 42956

Middle Eastern (MID) AF: 0.356 AC: 1513 AN: 4246

European-Non Finnish (NFE) AF: 0.423 AC: 327370 AN: 774526

Other (OTH) AF: 0.408 AC: 17923 AN: 43932

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.356 AC: 35699 AN: 100356 Hom.: 549 Cov.: 15 AF XY: 0.357 AC XY: 17225 AN XY: 48264

African (AFR) AF: 0.266 AC: 7182 AN: 27008

American (AMR) AF: 0.329 AC: 3076 AN: 9338

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 929 AN: 2432

East Asian (EAS) AF: 0.408 AC: 1171 AN: 2872

South Asian (SAS) AF: 0.353 AC: 866 AN: 2450

European-Finnish (FIN) AF: 0.405 AC: 2557 AN: 6320

Middle Eastern (MID) AF: 0.262 AC: 43 AN: 164

European-Non Finnish (NFE) AF: 0.401 AC: 19213 AN: 47910

Other (OTH) AF: 0.348 AC: 436 AN: 1252

Alfa AF: 0.358 Hom.: 188

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-1.1
PromoterAI		-0.0059	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2740086; hg19: chr8-7752127; COSMIC: COSV56362382;