rs17124508

Variant names:

• chr20-33274748-T-G
• rs17124508
• ENST00000423645.5:c.-42+1094T>G

Variant summary

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

The ENST00000423645.5(BPIFB1):​c.-42+1094T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,224 control chromosomes in the GnomAD database, including 352 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 0.064 (352 hom., cov: 32)
• Consequence: BPIFB1 ENST00000423645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.097 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+1094T>G		intron_variant	Intron 1 of 4	3		ENSP00000390471.1

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9715 AN: 152106 Hom.: 350 Cov.: 32

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0639 AC: 9728 AN: 152224 Hom.: 352 Cov.: 32 AF XY: 0.0626 AC XY: 4660 AN XY: 74430

African (AFR) AF: 0.0995 AC: 4132 AN: 41528

American (AMR) AF: 0.0354 AC: 542 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5178

South Asian (SAS) AF: 0.0342 AC: 165 AN: 4818

European-Finnish (FIN) AF: 0.0506 AC: 536 AN: 10596

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3851 AN: 68018

Other (OTH) AF: 0.0581 AC: 123 AN: 2116

Alfa AF: 0.0617 Hom.: 44

Bravo AF: 0.0636

Asia WGS AF: 0.0450 AC: 156 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	0.12
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17124508; hg19: chr20-31862554;