17-28619902-GGC-TGT

Variant names:

• chr17-28619902-GGC-TGT
• NM_014680.5:c.5476_5478delGCCinsACA
• BLTP2 p.Ala1826Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_014680.5(BLTP2):​c.5476_5478delGCCinsACA​(p.Ala1826Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BLTP2 NM_014680.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.20
• Publications: 0 publications found

Genes affected

BLTP2 (HGNC:28960): (bridge-like lipid transfer protein family member 2) This gene was initially characterized in human as having high expression levels in breast carcinomas and breast cancer cell lines. This gene also has increased expression in prostrate cancer cells relative to normal prostrate tissues. Expression of this gene is negatively regulated by direct binding of the microRNA miR-195 to its 3' UTR. miR-195 has been shown to modulate the invasiveness of prostrate cancer cells and xenograft metastases by downgrading expression of this gene. In mouse, the protein encoded by this gene was identified as an antigen on acute monocytic leukemia cells. In human, alternative splicing results in multiple transcript variants encoding distinct isoforms; some of these isoforms are predicted to contain an RNA pol II promoter FMP27 protein domain and a Golgi-body-localization APT1 domain. [provided by RefSeq, Apr 2017]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014680.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLTP2	NM_014680.5	MANE Select	c.5476_5478delGCCinsACA	p.Ala1826Thr	missense	N/A	NP_055495.2
	BLTP2	NM_001321560.2		c.5473_5475delGCCinsACA	p.Ala1825Thr	missense	N/A	NP_001308489.1
	BLTP2	NM_001363826.1		c.5047_5049delGCCinsACA	p.Ala1683Thr	missense	N/A	NP_001350755.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLTP2	ENST00000528896.7	TSL:1 MANE Select	c.5476_5478delGCCinsACA	p.Ala1826Thr	missense	N/A	ENSP00000436773.2	Q14667-1
	BLTP2	ENST00000939120.1		c.5473_5475delGCCinsACA	p.Ala1825Thr	missense	N/A	ENSP00000609179.1
	BLTP2	ENST00000939122.1		c.5473_5475delGCCinsACA	p.Ala1825Thr	missense	N/A	ENSP00000609181.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr17-26946920;