dbSNP rs2232582: LBP:p.Pro97Pro (chr20-38350862-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004139.5(LBP):c.291T>C(p.Pro97Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,612,716 control chromosomes in the GnomAD database, including 25,928 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 0.21 ( 4292 hom., cov: 33)

Exomes 𝑓: 0.16 ( 21636 hom. )

Consequence

LBP
NM_004139.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.89

Publications

22 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP7

Synonymous conserved (PhyloP=-2.89 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBP	NM_004139.5 link	c.291T>C	p.Pro97Pro	synonymous_variant	Exon 3 of 15	ENST00000217407.3	NP_004130.2	P18428Q8TCF0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBP	ENST00000217407.3 link	c.291T>C	p.Pro97Pro	synonymous_variant	Exon 3 of 15	1	NM_004139.5	ENSP00000217407.2		P18428

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32241

AN:

152160

Hom.:

4279

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.0811

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.185

GnomAD2 exomes

AF:

0.162

AC:

40549

AN:

250874

AF XY:

0.165

show subpopulations

Gnomad AFR exome

AF:

0.379

Gnomad AMR exome

AF:

0.0818

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.0892

Gnomad FIN exome

AF:

0.108

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.158

GnomAD4 exome

AF:

0.164

AC:

239943

AN:

1460438

Hom.:

21636

Cov.:

AF XY:

0.167

AC XY:

121171

AN XY:

726382

show subpopulations

African (AFR)

AF:

0.388

AC:

12983

AN:

33430

American (AMR)

AF:

0.0857

AC:

3831

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

4195

AN:

26116

East Asian (EAS)

AF:

0.0681

AC:

2701

AN:

39682

South Asian (SAS)

AF:

0.233

AC:

20050

AN:

86100

European-Finnish (FIN)

AF:

0.108

AC:

5772

AN:

53294

Middle Eastern (MID)

AF:

0.265

AC:

1523

AN:

5758

European-Non Finnish (NFE)

AF:

0.161

AC:

178743

AN:

1111046

Other (OTH)

AF:

0.168

AC:

10145

AN:

60316

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

9208

18416

27623

36831

46039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6494

12988

19482

25976

32470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.212

AC:

32296

AN:

152278

Hom.:

4292

Cov.:

AF XY:

0.210

AC XY:

15617

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.375

AC:

15574

AN:

41546

American (AMR)

AF:

0.134

AC:

2045

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

578

AN:

3472

East Asian (EAS)

AF:

0.0812

AC:

421

AN:

5182

South Asian (SAS)

AF:

0.234

AC:

1128

AN:

4830

European-Finnish (FIN)

AF:

0.102

AC:

1080

AN:

10610

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10943

AN:

68016

Other (OTH)

AF:

0.186

AC:

393

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1301

2603

3904

5206

6507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.177

Hom.:

2120

Bravo

AF:

0.217

Asia WGS

AF:

0.155

AC:

540

AN:

3478

EpiCase

AF:

0.164

EpiControl

AF:

0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.12

(source)

DANN

Benign

0.34

PhyloP100

-2.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over