ENST00000423645.5:c.-42+443G>A

Variant names:

• chr20-33274097-G-A
• rs8118144
• ENST00000423645.5:c.-42+443G>A

Variant summary

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

The ENST00000423645.5(BPIFB1):​c.-42+443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,206 control chromosomes in the GnomAD database, including 237 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 0.054 (237 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0634 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+443G>A		intron_variant	Intron 1 of 4	3		ENSP00000390471.1

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8224 AN: 152088 Hom.: 236 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0541 AC: 8233 AN: 152206 Hom.: 237 Cov.: 32 AF XY: 0.0529 AC XY: 3934 AN XY: 74404

African (AFR) AF: 0.0655 AC: 2720 AN: 41540

American (AMR) AF: 0.0323 AC: 494 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3466

East Asian (EAS) AF: 0.0358 AC: 185 AN: 5166

South Asian (SAS) AF: 0.0338 AC: 163 AN: 4820

European-Finnish (FIN) AF: 0.0505 AC: 534 AN: 10582

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

European-Non Finnish (NFE) AF: 0.0565 AC: 3841 AN: 68010

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0516 Hom.: 279

Bravo AF: 0.0521

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.68
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs8118144; hg19: chr20-31861903;