20-62259751-GGCACTGGAGCTCGCTGGGA-G

Position:

• chr20-62259751-GGCACTGGAGCTCGCTGGGA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_144498.4(OSBPL2):​c.38-227_38-209del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (12805 hom., cov: 0)
• Consequence: OSBPL2 NM_144498.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.894

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 20-62259751-GGCACTGGAGCTCGCTGGGA-G is Benign according to our data. Variant chr20-62259751-GGCACTGGAGCTCGCTGGGA-G is described in ClinVar as [Benign]. Clinvar id is 1259404.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL2	NM_144498.4	c.38-227_38-209del		intron_variant		ENST00000313733.9
OSBPL2	NM_001278649.3	c.-185+3533_-185+3551del		intron_variant
OSBPL2	NM_001363878.2	c.-329-227_-329-209del		intron_variant
OSBPL2	NM_014835.5	c.38-263_38-245del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL2	ENST00000313733.9	c.38-227_38-209del		intron_variant		1	NM_144498.4	P1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58528 AN: 151880 Hom.: 12810 Cov.: 0

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.385 AC: 58540 AN: 151998 Hom.: 12805 Cov.: 0 AF XY: 0.387 AC XY: 28760 AN XY: 74268

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.420

Alfa AF: 0.416 Hom.: 1717

Bravo AF: 0.379

Asia WGS AF: 0.519 AC: 1805 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 17, 2018

- -

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;