rs8118559

chr20-33274192-C-T

Variant summary

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

The ENST00000423645.5(BPIFB1):c.-42+538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,270 control chromosomes in the GnomAD database, including 161 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 (161 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFB1	ENST00000423645.5	c.-42+538C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6516 AN: 152152 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0428 AC: 6516 AN: 152270 Hom.: 161 Cov.: 32 AF XY: 0.0419 AC XY: 3120 AN XY: 74438

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.0270

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.0332

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0411

Alfa AF: 0.0487 Hom.: 164

Bravo AF: 0.0398

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	-0.94
Cadd	Benign	1.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8118559; hg19: chr20-31861998;