rs2057262

Positions:

• chr20-33099326-C-A
• chr20-33099326-C-G

Variant summary

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

The NM_182519.3(BPIFB4):​c.1570-1100C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,924 control chromosomes in the GnomAD database, including 25,227 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 0.57 (25227 hom., cov: 31)
• Consequence: BPIFB4 NM_182519.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

BPIFB4 (HGNC:16179): (BPI fold containing family B member 4) Predicted to enable lipid binding activity. Predicted to be located in cytoplasm and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPIFB4	NM_182519.3	c.1570-1100C>A		intron_variant		ENST00000375483.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPIFB4	ENST00000375483.4	c.1570-1100C>A		intron_variant		5	NM_182519.3	P1
BPIFB4	ENST00000674031.1	c.1936-1100C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86539 AN: 151806 Hom.: 25196 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.570 AC: 86633 AN: 151924 Hom.: 25227 Cov.: 31 AF XY: 0.563 AC XY: 41790 AN XY: 74252

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.582

Alfa AF: 0.585 Hom.: 11155

Bravo AF: 0.571

Asia WGS AF: 0.397 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.86
DANN	Benign	0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2057262; hg19: chr20-31687132;