rs6024905

Variant names:

• chr20-38329435-G-A
• rs6024905
• NM_001725.3:c.1230-1613G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.83).
• 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 rank	MANE	Protein	UniProt
BPI	NM_001725.3	c.1230-1613G>A		intron_variant	Intron 11 of 14	ENST00000642449.2	NP_001716.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPI	ENST00000642449.2	c.1230-1613G>A		intron_variant	Intron 11 of 14		NM_001725.3	ENSP00000494528.2

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

African (AFR) AF: 0.477 AC: 19781 AN: 41490

American (AMR) AF: 0.475 AC: 7258 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.145 AC: 753 AN: 5184

South Asian (SAS) AF: 0.438 AC: 2115 AN: 4826

European-Finnish (FIN) AF: 0.477 AC: 5043 AN: 10578

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.472 AC: 32064 AN: 67974

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.458 Hom.: 50393

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
PhyloP100		1.5
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: rs6024905; hg19: chr20-36957837;