Variant chr20-38309029-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001725.3(BPI):c.345C>T(p.Ser115=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00861 in 1,614,130 control chromosomes in the GnomAD database, including 91 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0065 ( 8 hom., cov: 33)

Exomes 𝑓: 0.0088 ( 83 hom. )

Consequence

BPI
NM_001725.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.751

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 -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 20-38309029-C-T is Benign according to our data. Variant chr20-38309029-C-T is described in ClinVar as [Benign]. Clinvar id is 774744.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.751 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
BPI	NM_001725.3 linkuse as main transcript	c.345C>T	p.Ser115=	synonymous_variant	3/15	ENST00000642449.2
BPI	XM_047440393.1 linkuse as main transcript	c.357C>T	p.Ser119=	synonymous_variant	3/13
BPI	XM_047440394.1 linkuse as main transcript	c.357C>T	p.Ser119=	synonymous_variant	3/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
BPI	ENST00000642449.2 linkuse as main transcript	c.345C>T	p.Ser115=	synonymous_variant	3/15		NM_001725.3	P1
BPI	ENST00000262865.9 linkuse as main transcript	c.357C>T	p.Ser119=	synonymous_variant	3/15	1
	ENST00000437016.1 linkuse as main transcript	n.183+17325G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00653

AC:

994

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00451

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00786

Gnomad ASJ

AF:

0.00835

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00456

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00842

Gnomad OTH

AF:

0.0125

GnomAD3 exomes

AF:

0.00627

AC:

1577

AN:

251466

Hom.:

AF XY:

0.00657

AC XY:

893

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.00406

Gnomad AMR exome

AF:

0.00437

Gnomad ASJ exome

AF:

0.00496

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00526

Gnomad FIN exome

AF:

0.00189

Gnomad NFE exome

AF:

0.00933

Gnomad OTH exome

AF:

0.00765

GnomAD4 exome

AF:

0.00883

AC:

12906

AN:

1461862

Hom.:

Cov.:

AF XY:

0.00884

AC XY:

6426

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.00400

Gnomad4 AMR exome

AF:

0.00523

Gnomad4 ASJ exome

AF:

0.00559

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00447

Gnomad4 FIN exome

AF:

0.00215

Gnomad4 NFE exome

AF:

0.0102

Gnomad4 OTH exome

AF:

0.00841

GnomAD4 genome

AF:

0.00652

AC:

993

AN:

152268

Hom.:

Cov.:

AF XY:

0.00606

AC XY:

451

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00450

Gnomad4 AMR

AF:

0.00785

Gnomad4 ASJ

AF:

0.00835

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00456

Gnomad4 FIN

AF:

0.00273

Gnomad4 NFE

AF:

0.00841

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00641

Hom.:

Bravo

AF:

0.00770

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.0101

EpiControl

AF:

0.0104

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.4

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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