Variant chr20-38360727-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_004139.5(LBP):c.612A>G(p.Ser204=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 1,611,950 control chromosomes in the GnomAD database, including 177,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.45 ( 15754 hom., cov: 31)

Exomes 𝑓: 0.46 ( 161288 hom. )

Consequence

LBP
NM_004139.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.648

Variant links:

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]

LBP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 20-38360727-A-G is Benign according to our data. Variant chr20-38360727-A-G is described in ClinVar as [Benign]. Clinvar id is 769469.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.648 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LBP	NM_004139.5 linkuse as main transcript	c.612A>G	p.Ser204=	synonymous_variant	6/15	ENST00000217407.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LBP	ENST00000217407.3 linkuse as main transcript	c.612A>G	p.Ser204=	synonymous_variant	6/15	1	NM_004139.5	P1

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68012

AN:

151878

Hom.:

15749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.623

Gnomad AMR

AF:

0.452

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.354

Gnomad FIN

AF:

0.550

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.494

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.464

AC:

676975

AN:

1459952

Hom.:

161288

Cov.:

AF XY:

0.462

AC XY:

335292

AN XY:

726406

show subpopulations

Gnomad4 AFR exome

AF:

0.387

Gnomad4 AMR exome

AF:

0.403

Gnomad4 ASJ exome

AF:

0.474

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.382

Gnomad4 FIN exome

AF:

0.548

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.444

GnomAD4 genome

AF:

0.448

AC:

68048

AN:

151998

Hom.:

15754

Cov.:

AF XY:

0.446

AC XY:

33127

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.390

Gnomad4 AMR

AF:

0.452

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.129

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.550

Gnomad4 NFE

AF:

0.494

Gnomad4 OTH

AF:

0.434

Alfa

AF:

0.466

Hom.:

22369

Bravo

AF:

0.434

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.047

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over