20-38334265-A-G

Variant names:

• chr20-38334265-A-G
• rs2275954
• NM_001725.3:c.1273-165A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPI	NM_001725.3	MANE Select	c.1273-165A>G		intron	N/A	NP_001716.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPI	ENST00000642449.2	MANE Select	c.1273-165A>G		intron	N/A	ENSP00000494528.2
	BPI	ENST00000262865.10	TSL:1	c.1162-165A>G		intron	N/A	ENSP00000262865.5
	BPI	ENST00000716802.1		c.1273-165A>G		intron	N/A	ENSP00000520600.1

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

African (AFR) AF: 0.735 AC: 30502 AN: 41492

American (AMR) AF: 0.522 AC: 7980 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1942 AN: 5182

South Asian (SAS) AF: 0.525 AC: 2529 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5189 AN: 10566

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34263 AN: 67948

Other (OTH) AF: 0.525 AC: 1109 AN: 2112

Alfa AF: 0.532 Hom.: 33829

Bravo AF: 0.569

Asia WGS AF: 0.428 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.38
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2275954; hg19: chr20-36962667;