20-33302031-C-T

Position:

• chr20-33302031-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• 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/exons	MANE	UniProt
BPIFB1	NM_033197.3	c.928-328C>T		intron_variant		ENST00000253354.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFB1	ENST00000253354.2	c.928-328C>T		intron_variant		1	NM_033197.3	P1
BPIFB1	ENST00000464032.1	n.556-328C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.0435

Gnomad4 SAS AF: 0.0374

Gnomad4 FIN AF: 0.0495

Gnomad4 NFE AF: 0.0488

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0494 Hom.: 63

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275082; hg19: chr20-31889837; COSMIC: COSV53605891;