rs6057810

Variant names:

• chr20-33282834-T-C
• rs6057810
• ENST00000423645.5:c.-41-3199T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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 = 0.268 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPIFB1	ENST00000423645.5	TSL:3	c.-41-3199T>C		intron	N/A	ENSP00000390471.1

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

African (AFR) AF: 0.273 AC: 11317 AN: 41530

American (AMR) AF: 0.0526 AC: 805 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3470

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5184

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4822

European-Finnish (FIN) AF: 0.0509 AC: 541 AN: 10626

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

European-Non Finnish (NFE) AF: 0.0571 AC: 3887 AN: 68030

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0855 Hom.: 258

Bravo AF: 0.121

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		0.21
PromoterAI		0.0031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6057810; hg19: chr20-31870640;