Variant chr20-38304274-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001725.3(BPI):c.51G>C(p.Leu17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,613,722 control chromosomes in the GnomAD database, including 226,407 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16331 hom., cov: 32)

Exomes 𝑓: 0.53 ( 210076 hom. )

Consequence

BPI
NM_001725.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.566

Variant links:

Genes affected

BPI (HGNC:1095): (bactericidal permeability increasing protein) This gene encodes a lipopolysaccharide binding protein. It is associated with human neutrophil granules and has antimicrobial activity against gram-negative organisms. [provided by RefSeq, Nov 2014]

BPI links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 20-38304274-G-C is Benign according to our data. Variant chr20-38304274-G-C is described in ClinVar as [Benign]. Clinvar id is 402431.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.566 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
BPI	NM_001725.3 linkuse as main transcript	c.51G>C	p.Leu17=	synonymous_variant	1/15	ENST00000642449.2	NP_001716.3
BPI	XM_047440393.1 linkuse as main transcript	c.63G>C	p.Leu21=	synonymous_variant	1/13		XP_047296349.1
BPI	XM_047440394.1 linkuse as main transcript	c.63G>C	p.Leu21=	synonymous_variant	1/12		XP_047296350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
BPI	ENST00000642449.2 linkuse as main transcript	c.51G>C	p.Leu17=	synonymous_variant	1/15		NM_001725.3	ENSP00000494528	P1
BPI	ENST00000262865.9 linkuse as main transcript	c.63G>C	p.Leu21=	synonymous_variant	1/15	1		ENSP00000262865
	ENST00000437016.1 linkuse as main transcript	n.184-14528C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66790

AN:

151934

Hom.:

16319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.569

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.501

GnomAD3 exomes

AF:

0.514

AC:

128765

AN:

250652

Hom.:

34096

AF XY:

0.517

AC XY:

70182

AN XY:

135668

show subpopulations

Gnomad AFR exome

AF:

0.205

Gnomad AMR exome

AF:

0.562

Gnomad ASJ exome

AF:

0.648

Gnomad EAS exome

AF:

0.553

Gnomad SAS exome

AF:

0.500

Gnomad FIN exome

AF:

0.444

Gnomad NFE exome

AF:

0.540

Gnomad OTH exome

AF:

0.550

GnomAD4 exome

AF:

0.532

AC:

777907

AN:

1461670

Hom.:

210076

Cov.:

AF XY:

0.531

AC XY:

386446

AN XY:

727140

show subpopulations

Gnomad4 AFR exome

AF:

0.206

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.655

Gnomad4 EAS exome

AF:

0.610

Gnomad4 SAS exome

AF:

0.501

Gnomad4 FIN exome

AF:

0.446

Gnomad4 NFE exome

AF:

0.542

Gnomad4 OTH exome

AF:

0.523

GnomAD4 genome

AF:

0.440

AC:

66837

AN:

152052

Hom.:

16331

Cov.:

AF XY:

0.439

AC XY:

32598

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.509

Gnomad4 ASJ

AF:

0.633

Gnomad4 EAS

AF:

0.569

Gnomad4 SAS

AF:

0.483

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.507

Alfa

AF:

0.523

Hom.:

12463

Bravo

AF:

0.442

Asia WGS

AF:

0.543

AC:

1891

AN:

3478

EpiCase

AF:

0.562

EpiControl

AF:

0.563

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

1.7

DANN

Benign

0.58

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

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