rs200674528

Variant names:

• chr3-31748045-T-A
• rs200674528
• NM_017784.5:c.805A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-31748045-T-A
• chr3-31748045-T-C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_017784.5(OSBPL10):​c.805A>T​(p.Thr269Ser) 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. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T269A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: OSBPL10 NM_017784.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.28
• Publications: 1 publications found

Genes affected

OSBPL10 (HGNC:16395): (oxysterol binding protein like 10) 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. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14448154).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL10	NM_017784.5	c.805A>T	p.Thr269Ser	missense_variant	Exon 5 of 12	ENST00000396556.7	NP_060254.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL10	ENST00000396556.7	c.805A>T	p.Thr269Ser	missense_variant	Exon 5 of 12	1	NM_017784.5	ENSP00000379804.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	19
DANN	Benign	0.25
DEOGEN2	Benign	0.0072	T;.;T
Eigen	Benign	-0.33
Eigen_PC	Benign	-0.088
FATHMM_MKL	Uncertain	0.76	D
LIST_S2	Benign	0.74	T;T;T
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.14	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.41	N;.;.
PhyloP100		5.3
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	0.21	N;N;N
REVEL	Benign	0.085
Sift	Benign	0.59	T;T;T
Sift4G	Benign	1.0	T;T;T
Polyphen		0.0060	B;.;.
Vest4		0.056
MutPred		0.27		Loss of glycosylation at S265 (P = 0.0302);.;.;
MVP		0.51
MPC		0.23
ClinPred		0.41	T
GERP RS		5.6
Varity_R		0.084
gMVP		0.11
Mutation Taster		=90/10	polymorphism

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

Other links and lift over

dbSNP: rs200674528; hg19: chr3-31789537;