17-47815322-G-A

Variant names:

• chr17-47815322-G-A
• NM_145798.3:c.1150C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145798.3(OSBPL7):​c.1150C>T​(p.Leu384Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: OSBPL7 NM_145798.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.00

Genes affected

OSBPL7 (HGNC:16387): (oxysterol binding protein like 7) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Like most members, the encoded protein contains an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. Two transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19088215).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL7	NM_145798.3	c.1150C>T	p.Leu384Phe	missense_variant	Exon 13 of 23	ENST00000007414.8	NP_665741.1
OSBPL7	XM_047435292.1	c.1150C>T	p.Leu384Phe	missense_variant	Exon 13 of 23		XP_047291248.1
OSBPL7	XM_047435293.1	c.1096C>T	p.Leu366Phe	missense_variant	Exon 12 of 22		XP_047291249.1
OSBPL7	XR_934362.2	n.1366C>T		non_coding_transcript_exon_variant	Exon 13 of 22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL7	ENST00000007414.8	c.1150C>T	p.Leu384Phe	missense_variant	Exon 13 of 23	1	NM_145798.3	ENSP00000007414.3
OSBPL7	ENST00000613735.4	n.*245+16C>T		intron_variant	Intron 12 of 15	1		ENSP00000479827.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 01, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1150C>T (p.L384F) alteration is located in exon 13 (coding exon 12) of the OSBPL7 gene. This alteration results from a C to T substitution at nucleotide position 1150, causing the leucine (L) at amino acid position 384 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.084	T
BayesDel_noAF	Benign	-0.36
CADD	Uncertain	24
DANN	Benign	0.97
DEOGEN2	Benign	0.23	T;T
Eigen	Benign	0.035
Eigen_PC	Benign	0.13
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Benign	0.81	.;T
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.19	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.6	M;M
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-2.7	D;D
REVEL	Benign	0.094
Sift	Uncertain	0.0030	D;D
Sift4G	Uncertain	0.035	D;D
Polyphen		0.15	B;B
Vest4		0.43
MutPred		0.20		Gain of helix (P = 0.0496);Gain of helix (P = 0.0496);
MVP		0.46
MPC		0.65
ClinPred		0.87	D
GERP RS		3.8
Varity_R		0.19

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-45892688;