dbSNP rs5743418: GS1-24F4.2:n.226-7084G>A (chr8-6878038-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000531701.1(GS1-24F4.2):n.226-7084G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 590,882 control chromosomes in the GnomAD database, including 418 homozygotes. 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 0.021 ( 71 hom., cov: 32)

Exomes 𝑓: 0.028 ( 347 hom. )

Consequence

GS1-24F4.2
ENST00000531701.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0860

Variant links:

Genes affected

GS1-24F4.2 (HGNC:):

GS1-24F4.2 links:

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]

DEFB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEFB1	NM_005218.4 link	c.-181C>T		upstream_gene_variant		ENST00000297439.4	NP_005209.1	P60022

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1 link	n.226-7084G>A		intron_variant	Intron 2 of 2	3
DEFB1	ENST00000297439.4 link	c.-181C>T		upstream_gene_variant		1	NM_005218.4	ENSP00000297439.3		P60022

Frequencies

GnomAD3 genomes

AF:

0.0211

AC:

3212

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0160

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0169

Gnomad ASJ

AF:

0.104

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0739

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0209

Gnomad OTH

AF:

0.0287

GnomAD4 exome

AF:

0.0276

AC:

12105

AN:

438612

Hom.:

347

Cov.:

AF XY:

0.0311

AC XY:

7276

AN XY:

233758

show subpopulations

Gnomad4 AFR exome

AF:

0.0165

Gnomad4 AMR exome

AF:

0.0162

Gnomad4 ASJ exome

AF:

0.105

Gnomad4 EAS exome

AF:

0.000143

Gnomad4 SAS exome

AF:

0.0772

Gnomad4 FIN exome

AF:

0.00462

Gnomad4 NFE exome

AF:

0.0212

Gnomad4 OTH exome

AF:

0.0314

GnomAD4 genome

AF:

0.0211

AC:

3210

AN:

152270

Hom.:

Cov.:

AF XY:

0.0215

AC XY:

1601

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0160

Gnomad4 AMR

AF:

0.0169

Gnomad4 ASJ

AF:

0.104

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0742

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.0209

Gnomad4 OTH

AF:

0.0284

Alfa

AF:

0.0236

Hom.:

Bravo

AF:

0.0207

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

DANN

Benign

0.61

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