rs45442801

Variant names:

• chr8-6870512-G-A
• rs45442801
• ENST00000657010.1:n.1431G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-6870512-G-A
• chr8-6870512-G-C
• chr8-6870512-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000657010.1(GS1-24F4.2):​n.1431G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00273 in 778,678 control chromosomes in the GnomAD database, including 61 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 0.0017 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (52 hom.)
• Consequence: GS1-24F4.2 ENST00000657010.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.41

Genes affected

GS1-24F4.2 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0017 (259/151916) while in subpopulation SAS AF= 0.0476 (229/4810). AF 95% confidence interval is 0.0426. There are 9 homozygotes in gnomad4. There are 191 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEFB1	NM_005218.4	c.*169C>T		downstream_gene_variant		ENST00000297439.4	NP_005209.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000657010.1	n.1431G>A		non_coding_transcript_exon_variant	Exon 5 of 5
GS1-24F4.2	ENST00000531701.1	n.226-14610G>A		intron_variant	Intron 2 of 2	3
GS1-24F4.2	ENST00000655804.1	n.323-2669G>A		intron_variant	Intron 2 of 2
DEFB1	ENST00000297439.4	c.*169C>T		downstream_gene_variant		1	NM_005218.4	ENSP00000297439.3

Frequencies

GnomAD3 genomes AF: 0.00170 AC: 258 AN: 151806 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000265

Gnomad OTH AF: 0.00144

GnomAD4 exome AF: 0.00297 AC: 1864 AN: 626762 Hom.: 52 AF XY: 0.00422 AC XY: 1352 AN XY: 320188

Gnomad4 AFR exome AF: 0.000325

Gnomad4 AMR exome AF: 0.000121

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000981

Gnomad4 SAS exome AF: 0.0369

Gnomad4 FIN exome AF: 0.0000342

Gnomad4 NFE exome AF: 0.000190

Gnomad4 OTH exome AF: 0.00280

GnomAD4 genome AF: 0.00170 AC: 259 AN: 151916 Hom.: 9 Cov.: 32 AF XY: 0.00257 AC XY: 191 AN XY: 74220

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000265

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.0000694 Hom.: 0

Bravo AF: 0.000502

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45442801; hg19: chr8-6728034;