rs6120141

Variant names:

• chr20-33180849-T-C
• rs6120141
• NM_080574.4:c.*37+252T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BPIFA2	NM_080574.4	c.*37+252T>C		intron_variant	Intron 8 of 8	ENST00000354932.6	NP_542141.1
BPIFA2	NM_001319164.2	c.*37+252T>C		intron_variant	Intron 8 of 8		NP_001306093.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFA2	ENST00000354932.6	c.*37+252T>C		intron_variant	Intron 8 of 8	1	NM_080574.4	ENSP00000347012.5
BPIFA2	ENST00000253362.6	c.*37+252T>C		intron_variant	Intron 8 of 8	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

African (AFR) AF: 0.365 AC: 15142 AN: 41454

American (AMR) AF: 0.0570 AC: 872 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3470

East Asian (EAS) AF: 0.0602 AC: 312 AN: 5184

South Asian (SAS) AF: 0.0147 AC: 71 AN: 4834

European-Finnish (FIN) AF: 0.0403 AC: 428 AN: 10612

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0345 AC: 2347 AN: 68006

Other (OTH) AF: 0.0988 AC: 209 AN: 2116

Alfa AF: 0.100 Hom.: 310

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
PhyloP100		-0.64
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: rs6120141; hg19: chr20-31768655;