ENST00000423645.5:c.-42+4405G>T

Variant names:

• chr20-33278059-G-T
• rs8115852
• ENST00000423645.5:c.-42+4405G>T

Variant summary

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

The ENST00000423645.5(BPIFB1):​c.-42+4405G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,100 control chromosomes in the GnomAD database, including 2,007 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 0.12 (2007 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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+4405G>T		intron_variant	Intron 1 of 4	3		ENSP00000390471.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18305 AN: 151982 Hom.: 1998 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.121 AC: 18347 AN: 152100 Hom.: 2007 Cov.: 32 AF XY: 0.117 AC XY: 8703 AN XY: 74360

African (AFR) AF: 0.294 AC: 12206 AN: 41462

American (AMR) AF: 0.0577 AC: 882 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3470

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5170

South Asian (SAS) AF: 0.0344 AC: 165 AN: 4796

European-Finnish (FIN) AF: 0.0510 AC: 541 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0580 AC: 3943 AN: 68000

Other (OTH) AF: 0.100 AC: 211 AN: 2104

Alfa AF: 0.0400 Hom.: 55

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8115852; hg19: chr20-31865865;