rs6024905

chr20-38329435-G-A

Variant summary

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

The NM_001725.3(BPI):c.1230-1613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,114 control chromosomes in the GnomAD database, including 16,618 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 0.46 (16618 hom., cov: 33)
• Consequence: BPI NM_001725.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPI	NM_001725.3	c.1230-1613G>A		intron_variant		ENST00000642449.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPI	ENST00000642449.2	c.1230-1613G>A		intron_variant			NM_001725.3	P1
BPI	ENST00000262865.9	c.1242-1613G>A		intron_variant		1
BPI	ENST00000417318.3	c.639-1613G>A		intron_variant		5
BPI	ENST00000489102.2	c.*419-1613G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70219 AN: 151994 Hom.: 16602 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.462 AC: 70283 AN: 152114 Hom.: 16618 Cov.: 33 AF XY: 0.460 AC XY: 34177 AN XY: 74376

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.444

Alfa AF: 0.453 Hom.: 19118

Bravo AF: 0.461

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	9.4
Dann	Benign	0.61

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: rs6024905; hg19: chr20-36957837;