rs2275954

Positions:

• chr20-38334265-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001725.3(BPI):​c.1273-165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,070 control chromosomes in the GnomAD database, including 25,210 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 0.56 (25210 hom., cov: 32)
• Consequence: BPI NM_001725.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPI	NM_001725.3	c.1273-165A>G		intron_variant		ENST00000642449.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPI	ENST00000642449.2	c.1273-165A>G		intron_variant			NM_001725.3	P1
BPI	ENST00000262865.9	c.1285-165A>G		intron_variant		1
BPI	ENST00000417318.3	c.682-165A>G		intron_variant		5
BPI	ENST00000489102.2	c.*462-165A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85775 AN: 151952 Hom.: 25171 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.526

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 85874 AN: 152070 Hom.: 25210 Cov.: 32 AF XY: 0.560 AC XY: 41620 AN XY: 74322

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.525

Alfa AF: 0.507 Hom.: 19544

Bravo AF: 0.569

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs2275954; hg19: chr20-36962667;