NM_144498.4:c.38-227_38-209dupACTGGAGCTCGCTGGGAGC

Variant names:

• chr20-62259751-G-GGCACTGGAGCTCGCTGGGA
• rs3215942
• NM_144498.4:c.38-227_38-209dupACTGGAGCTCGCTGGGAGC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_144498.4(OSBPL2):​c.38-227_38-209dupACTGGAGCTCGCTGGGAGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: OSBPL2 NM_144498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

OSBPL2 (HGNC:15761): (oxysterol binding protein like 2) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain, although the encoded protein contains only the sterol-binding domain. In vitro studies have shown that the encoded protein can bind strongly to phosphatic acid and weakly to phosphatidylinositol 3-phosphate, but cannot bind to 25-hydroxycholesterol. The protein associates with the Golgi apparatus. Transcript variants encoding different isoforms have been described. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL2	NM_144498.4	c.38-227_38-209dupACTGGAGCTCGCTGGGAGC		intron_variant	Intron 2 of 13	ENST00000313733.9	NP_653081.1
OSBPL2	NM_014835.5	c.38-263_38-245dupACTGGAGCTCGCTGGGAGC		intron_variant	Intron 2 of 13		NP_055650.1
OSBPL2	NM_001363878.2	c.-329-227_-329-209dupACTGGAGCTCGCTGGGAGC		intron_variant	Intron 2 of 14		NP_001350807.1
OSBPL2	NM_001278649.3	c.-185+3533_-185+3551dupACTGGAGCTCGCTGGGAGC		intron_variant	Intron 2 of 12		NP_001265578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL2	ENST00000313733.9	c.38-230_38-229insGCACTGGAGCTCGCTGGGA		intron_variant	Intron 2 of 13	1	NM_144498.4	ENSP00000316649.3

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3215942; hg19: chr20-60834807;