rs6120141

Positions:

• chr20-33180849-T-C

Variant summary

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

The NM_080574.4(BPIFA2):​c.*37+252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,184 control chromosomes in the GnomAD database, including 2,931 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 0.13 (2931 hom., cov: 32)
• Consequence: BPIFA2 NM_080574.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

BPIFA2 (HGNC:16203): (BPI fold containing family A member 2) This gene encodes a member of the palate, lung and nasal epithelium clone (Plunc) family of proteins. Members of this family have been proposed to play a role in the local antibacterial response in nose, mouth and upper respiratory pathways. The encoded soluble salivary protein binds bacterial lipopolysaccharide (LPS) and inhibits bacterial growth. This gene is present in a gene cluster on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPIFA2	NM_080574.4	c.*37+252T>C		intron_variant		ENST00000354932.6	NP_542141.1
BPIFA2	NM_001319164.2	c.*37+252T>C		intron_variant			NP_001306093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BPIFA2	ENST00000354932.6	c.*37+252T>C		intron_variant		1	NM_080574.4	ENSP00000347012.5
BPIFA2	ENST00000253362.6	c.*37+252T>C		intron_variant		1		ENSP00000253362.2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19459 AN: 152066 Hom.: 2931 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.128 AC: 19484 AN: 152184 Hom.: 2931 Cov.: 32 AF XY: 0.124 AC XY: 9212 AN XY: 74422

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0345

Gnomad4 OTH AF: 0.0988

Alfa AF: 0.0916 Hom.: 257

Bravo AF: 0.140

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.45

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: rs6120141; hg19: chr20-31768655;