rs17307318

Variant names:

• chr20-33275851-A-G
• rs17307318
• ENST00000423645.5:c.-42+2197A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423645.5(BPIFB1):​c.-42+2197A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,214 control chromosomes in the GnomAD database, including 160 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 0.043 (160 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 4 publications found

Genes affected

BPIFB1 (HGNC:16108): (BPI fold containing family B member 1) The protein encoded by this gene may be involved in the innate immune response to bacterial exposure in the mouth, nasal cavities, and lungs. The encoded protein is secreted and is a member of the BPI/LBP/PLUNC protein superfamily. This gene is found with other members of the superfamily in a cluster on chromosome 20. [provided by RefSeq, Jul 2008]

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 (NFE) allele frequency at 95% confidence interval = 0.0549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFB1	ENST00000423645.5	c.-42+2197A>G		intron_variant	Intron 1 of 4	3		ENSP00000390471.1

Frequencies

GnomAD3 genomes AF: 0.0430 AC: 6533 AN: 152096 Hom.: 160 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.0508

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0429 AC: 6533 AN: 152214 Hom.: 160 Cov.: 32 AF XY: 0.0421 AC XY: 3136 AN XY: 74418

African (AFR) AF: 0.0269 AC: 1118 AN: 41538

American (AMR) AF: 0.0275 AC: 420 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.0350 AC: 181 AN: 5166

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4824

European-Finnish (FIN) AF: 0.0508 AC: 539 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0564 AC: 3834 AN: 67996

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0440 Hom.: 31

Bravo AF: 0.0400

Asia WGS AF: 0.0400 AC: 138 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	3.4
DANN	Benign	0.72
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17307318; hg19: chr20-31863657;