NM_182519.3:c.1570-1100C>A

Variant names:

• chr20-33099326-C-A
• rs2057262
• NM_182519.3:c.1570-1100C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BPIFB4	NM_182519.3	c.1570-1100C>A		intron_variant	Intron 13 of 17	ENST00000375483.4	NP_872325.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFB4	ENST00000375483.4	c.1570-1100C>A		intron_variant	Intron 13 of 17	5	NM_182519.3	ENSP00000364632.3
BPIFB4	ENST00000674031.1	c.1936-1100C>A		intron_variant	Intron 10 of 14			ENSP00000501266.1

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

African (AFR) AF: 0.546 AC: 22608 AN: 41408

American (AMR) AF: 0.568 AC: 8684 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2521 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1150 AN: 5146

South Asian (SAS) AF: 0.489 AC: 2348 AN: 4804

European-Finnish (FIN) AF: 0.528 AC: 5573 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41761 AN: 67952

Other (OTH) AF: 0.582 AC: 1227 AN: 2110

Alfa AF: 0.589 Hom.: 12790

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
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2057262; hg19: chr20-31687132;