chr3-31923406-G-A

Position:

• chr3-31923406-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017784.5(OSBPL10):​c.282-43576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,996 control chromosomes in the GnomAD database, including 30,521 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 0.63 (30521 hom., cov: 32)
• Consequence: OSBPL10 NM_017784.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL10	NM_017784.5	c.282-43576C>T		intron_variant		ENST00000396556.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL10	ENST00000396556.7	c.282-43576C>T		intron_variant		1	NM_017784.5	P2

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95612 AN: 151878 Hom.: 30509 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.629 AC: 95669 AN: 151996 Hom.: 30521 Cov.: 32 AF XY: 0.630 AC XY: 46807 AN XY: 74264

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.643

Alfa AF: 0.645 Hom.: 41639

Bravo AF: 0.626

Asia WGS AF: 0.791 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.64

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

LitVar

Other links and lift over

dbSNP: rs7644177; hg19: chr3-31964898;