rs2232578

Variant names:

• chr20-38346312-G-A
• rs2232578
• NM_004139.5:c.-205G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-38346312-G-A
• chr20-38346312-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004139.5(LBP):​c.-205G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 575,976 control chromosomes in the GnomAD database, including 177,204 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 0.76 (44038 hom., cov: 32)
  • Exomes 𝑓: 0.79 (133166 hom.)
• Consequence: LBP NM_004139.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

LBP (HGNC:6517): (lipopolysaccharide binding protein) The protein encoded by this gene is involved in the acute-phase immunologic response to gram-negative bacterial infections. Gram-negative bacteria contain a glycolipid, lipopolysaccharide (LPS), on their outer cell wall. Together with bactericidal permeability-increasing protein (BPI), the encoded protein binds LPS and interacts with the CD14 receptor, probably playing a role in regulating LPS-dependent monocyte responses. Studies in mice suggest that the encoded protein is necessary for the rapid acute-phase response to LPS but not for the clearance of LPS from circulation. This protein is part of a family of structurally and functionally related proteins, including BPI, plasma cholesteryl ester transfer protein (CETP), and phospholipid transfer protein (PLTP). [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBP	NM_004139.5	c.-205G>A		upstream_gene_variant		ENST00000217407.3	NP_004130.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBP	ENST00000217407.3	c.-205G>A		upstream_gene_variant		1	NM_004139.5	ENSP00000217407.2

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115082 AN: 151944 Hom.: 44023 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.779

GnomAD4 exome AF: 0.790 AC: 334886 AN: 423914 Hom.: 133166 Cov.: 5 AF XY: 0.783 AC XY: 174252 AN XY: 222596

Gnomad4 AFR exome AF: 0.644

Gnomad4 AMR exome AF: 0.836

Gnomad4 ASJ exome AF: 0.768

Gnomad4 EAS exome AF: 0.789

Gnomad4 SAS exome AF: 0.671

Gnomad4 FIN exome AF: 0.837

Gnomad4 NFE exome AF: 0.812

Gnomad4 OTH exome AF: 0.784

GnomAD4 genome AF: 0.757 AC: 115141 AN: 152062 Hom.: 44038 Cov.: 32 AF XY: 0.757 AC XY: 56265 AN XY: 74340

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.777

Alfa AF: 0.798 Hom.: 54631

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2232578; hg19: chr20-36974715;