rs6057810

chr20-33282834-T-C

Variant summary

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

The ENST00000423645.5(BPIFB1):c.-41-3199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,288 control chromosomes in the GnomAD database, including 1,762 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 0.11 (1762 hom., cov: 33)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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.-41-3199T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17275 AN: 152170 Hom.: 1756 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.0366

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.114 AC: 17308 AN: 152288 Hom.: 1762 Cov.: 33 AF XY: 0.111 AC XY: 8251 AN XY: 74464

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0571

Gnomad4 OTH AF: 0.0945

Alfa AF: 0.0820 Hom.: 226

Bravo AF: 0.121

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6057810; hg19: chr20-31870640;