Variant rs17304572 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080574.4(BPIFA2):c.337A>G(p.Lys113Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00849 in 1,614,144 control chromosomes in the GnomAD database, including 198 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0083 ( 18 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 180 hom. )

Consequence

BPIFA2
NM_080574.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.417

Variant links:

Genes affected

BPIFA2 (HGNC:16203): (BPI fold containing family A member 2) This gene encodes a member of the palate, lung and nasal epithelium clone (Plunc) family of proteins. Members of this family have been proposed to play a role in the local antibacterial response in nose, mouth and upper respiratory pathways. The encoded soluble salivary protein binds bacterial lipopolysaccharide (LPS) and inhibits bacterial growth. This gene is present in a gene cluster on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

BPIFA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026183426).

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPIFA2	NM_080574.4 linkuse as main transcript	c.337A>G	p.Lys113Glu	missense_variant	4/9	ENST00000354932.6	NP_542141.1
BPIFA2	NM_001319164.2 linkuse as main transcript	c.337A>G	p.Lys113Glu	missense_variant	4/9		NP_001306093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BPIFA2	ENST00000354932.6 linkuse as main transcript	c.337A>G	p.Lys113Glu	missense_variant	4/9	1	NM_080574.4	ENSP00000347012	P1
BPIFA2	ENST00000253362.6 linkuse as main transcript	c.337A>G	p.Lys113Glu	missense_variant	4/9	1		ENSP00000253362	P1

Frequencies

GnomAD3 genomes

AF:

0.00821

AC:

1250

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00251

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0403

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00217

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00707

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.0146

AC:

3680

AN:

251474

Hom.:

122

AF XY:

0.0119

AC XY:

1613

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.00215

Gnomad AMR exome

AF:

0.0754

Gnomad ASJ exome

AF:

0.000397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00140

Gnomad FIN exome

AF:

0.00249

Gnomad NFE exome

AF:

0.00763

Gnomad OTH exome

AF:

0.0112

GnomAD4 exome

AF:

0.00851

AC:

12439

AN:

1461846

Hom.:

180

Cov.:

AF XY:

0.00786

AC XY:

5719

AN XY:

727222

show subpopulations

Gnomad4 AFR exome

AF:

0.00140

Gnomad4 AMR exome

AF:

0.0732

Gnomad4 ASJ exome

AF:

0.000574

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00147

Gnomad4 FIN exome

AF:

0.00324

Gnomad4 NFE exome

AF:

0.00754

Gnomad4 OTH exome

AF:

0.00694

GnomAD4 genome

AF:

0.00827

AC:

1260

AN:

152298

Hom.:

Cov.:

AF XY:

0.00823

AC XY:

613

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00250

Gnomad4 AMR

AF:

0.0409

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00217

Gnomad4 NFE

AF:

0.00707

Gnomad4 OTH

AF:

0.00852

Alfa

AF:

0.00840

Hom.:

Bravo

AF:

0.0119

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.00204

AC:

ESP6500EA

AF:

0.00756

AC:

ExAC

AF:

0.0129

AC:

1562

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.00480

EpiControl

AF:

0.00622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.00071

T;T

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.82

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.34

.;T

MetaRNN

Benign

0.0026

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.5

L;L

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.71

N;N

REVEL

Benign

0.030

Sift

Benign

0.072

T;T

Sift4G

Benign

0.096

T;T

Polyphen

0.76

P;P

Vest4

0.040

MPC

0.46

ClinPred

0.023

GERP RS

0.54

Varity_R

0.072

gMVP

0.12

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over