rs8118559

Variant names:

• chr20-33274192-C-T
• rs8118559
• ENST00000960538.1:c.-93+538C>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+538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0428 in 152,270 control chromosomes in the GnomAD database, including 161 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 0.043 (161 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423645.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFB1	ENST00000960538.1		c.-93+538C>T		intron	N/A	ENSP00000630597.1
	BPIFB1	ENST00000423645.5	TSL:3	c.-42+538C>T		intron	N/A	ENSP00000390471.1	A2A2R0

Frequencies

GnomAD3 genomes AF: 0.0428 AC: 6516 AN: 152152 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0401

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

GnomAD4 genome AF: 0.0428 AC: 6516 AN: 152270 Hom.: 161 Cov.: 32 AF XY: 0.0419 AC XY: 3120 AN XY: 74438

African (AFR) AF: 0.0269 AC: 1118 AN: 41554

American (AMR) AF: 0.0270 AC: 413 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5174

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4818

European-Finnish (FIN) AF: 0.0505 AC: 536 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0562 AC: 3824 AN: 68018

Other (OTH) AF: 0.0411 AC: 87 AN: 2116

Alfa AF: 0.0480 Hom.: 203

Bravo AF: 0.0398

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs8118559; hg19: chr20-31861998;