rs9880436

Variant names:

• chr3-31831722-T-C
• rs9880436
• NM_017784.5:c.538-1491A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-31831722-T-C
• chr3-31831722-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017784.5(OSBPL10):​c.538-1491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,982 control chromosomes in the GnomAD database, including 16,069 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (16069 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017784.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	NM_017784.5	MANE Select	c.538-1491A>G		intron	N/A	NP_060254.2
	OSBPL10	NM_001174060.2		c.537+44711A>G		intron	N/A	NP_001167531.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL10	ENST00000396556.7	TSL:1 MANE Select	c.538-1491A>G		intron	N/A	ENSP00000379804.2
	OSBPL10	ENST00000438237.6	TSL:2	c.537+44711A>G		intron	N/A	ENSP00000406124.2
	OSBPL10	ENST00000698199.1		c.538-1491A>G		intron	N/A	ENSP00000513603.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68850 AN: 151864 Hom.: 16062 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.453 AC: 68894 AN: 151982 Hom.: 16069 Cov.: 32 AF XY: 0.457 AC XY: 33908 AN XY: 74276

African (AFR) AF: 0.347 AC: 14356 AN: 41420

American (AMR) AF: 0.563 AC: 8601 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1778 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1657 AN: 5166

South Asian (SAS) AF: 0.509 AC: 2453 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5105 AN: 10560

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33319 AN: 67956

Other (OTH) AF: 0.477 AC: 1009 AN: 2114

Alfa AF: 0.481 Hom.: 58906

Bravo AF: 0.453

Asia WGS AF: 0.411 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.9
DANN	Benign	0.74
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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: rs9880436; hg19: chr3-31873214;