20-38318446-G-T

Variant names:

• chr20-38318446-G-T
• rs4358188
• NM_001725.3:c.634G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001725.3(BPI):​c.634G>T​(p.Glu212*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BPI NM_001725.3 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 59 publications found

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]

ENSG00000206249 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001725.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPI	NM_001725.3	MANE Select	c.634G>T	p.Glu212*	stop_gained	Exon 6 of 15	NP_001716.3	A0A2R8YDF1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPI	ENST00000642449.2	MANE Select	c.634G>T	p.Glu212*	stop_gained	Exon 6 of 15	ENSP00000494528.2	A0A2R8YDF1
	BPI	ENST00000262865.10	TSL:1	c.634G>T	p.Glu212*	stop_gained	Exon 9 of 16	ENSP00000262865.5	P17213
	BPI	ENST00000716802.1		c.634G>T	p.Glu212*	stop_gained	Exon 8 of 17	ENSP00000520600.1	A0A2R8YDF1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 53

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 49407

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.25
CADD	Pathogenic	28
DANN	Uncertain	0.99
Eigen	Benign	-0.24
Eigen_PC	Benign	-0.58
FATHMM_MKL	Benign	0.012	N
PhyloP100		-1.1
Vest4		0.93
GERP RS		0.59
Mutation Taster		=43/157	disease causing (fs/PTC)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4358188; hg19: chr20-36946848;