20-33302031-C-T

Variant names:

• chr20-33302031-C-T
• rs2275082
• NM_033197.3:c.928-328C>T

Variant summary

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

The NM_033197.3(BPIFB1):​c.928-328C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0544 in 152,130 control chromosomes in the GnomAD database, including 242 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 (242 hom., cov: 32)
• Consequence: BPIFB1 NM_033197.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFB1	NM_033197.3	c.928-328C>T		intron_variant	Intron 9 of 15	ENST00000253354.2	NP_149974.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFB1	ENST00000253354.2	c.928-328C>T		intron_variant	Intron 9 of 15	1	NM_033197.3	ENSP00000253354.1
BPIFB1	ENST00000464032.1	n.556-328C>T		intron_variant	Intron 4 of 12	5

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8286 AN: 152012 Hom.: 242 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0544 AC: 8282 AN: 152130 Hom.: 242 Cov.: 32 AF XY: 0.0535 AC XY: 3977 AN XY: 74378

African (AFR) AF: 0.0794 AC: 3295 AN: 41478

American (AMR) AF: 0.0314 AC: 480 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3472

East Asian (EAS) AF: 0.0435 AC: 225 AN: 5176

South Asian (SAS) AF: 0.0374 AC: 180 AN: 4818

European-Finnish (FIN) AF: 0.0495 AC: 525 AN: 10600

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0488 AC: 3319 AN: 67980

Other (OTH) AF: 0.0474 AC: 100 AN: 2110

Alfa AF: 0.0490 Hom.: 106

Bravo AF: 0.0537

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.72
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs2275082; hg19: chr20-31889837; COSMIC: COSV53605891;