rs750064

Variant names:

• chr20-33235824-T-A
• rs750064
• NM_130852.3:c.-242T>A

Your query was ambiguous. Multiple possible variants found:

• chr20-33235824-T-A
• chr20-33235824-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_130852.3(BPIFA1):​c.-242T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: BPIFA1 NM_130852.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

BPIFA1 (HGNC:15749): (BPI fold containing family A member 1) This gene is the human homolog of murine plunc, and like the mouse gene, is specifically expressed in the upper airways and nasopharyngeal regions. The encoded antimicrobial protein displays antibacterial activity against Gram-negative bacteria. It is thought to be involved in inflammatory responses to irritants in the upper airways and may also serve as a potential molecular marker for detection of micrometastasis in non-small-cell lung cancer. Multiple transcript variants resulting from alternative splicing in the 3' UTR have been detected, but the full-length nature of only three are known. [provided by RefSeq, Aug 2014]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BPIFA1	NM_130852.3	c.-242T>A		upstream_gene_variant		ENST00000354297.9	NP_570913.1
BPIFA1	NM_001243193.2	c.-242T>A		upstream_gene_variant			NP_001230122.1
BPIFA1	NM_016583.4	c.-242T>A		upstream_gene_variant			NP_057667.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BPIFA1	ENST00000354297.9	c.-242T>A		upstream_gene_variant		1	NM_130852.3	ENSP00000346251.4
BPIFA1	ENST00000375413.8	c.-242T>A		upstream_gene_variant		1		ENSP00000364562.4
BPIFA1	ENST00000375422.6	c.-242T>A		upstream_gene_variant		1		ENSP00000364571.2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750064; hg19: chr20-31823630;