rs1434087

Variant names:

• chr2-178339070-G-A
• rs1434087
• NM_032523.4:c.870G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-178339070-G-A
• chr2-178339070-G-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_032523.4(OSBPL6):​c.870G>A​(p.Ser290Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 1,610,878 control chromosomes in the GnomAD database, including 677,525 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 0.91 (63527 hom., cov: 32)
  • Exomes 𝑓: 0.92 (613998 hom.)
• Consequence: OSBPL6 NM_032523.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

OSBPL6 (HGNC:16388): (oxysterol binding protein like 6) 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. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BP7: Synonymous conserved (PhyloP=1.25 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL6	NM_032523.4	c.870G>A	p.Ser290Ser	synonymous_variant	Exon 10 of 25	ENST00000190611.9	NP_115912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL6	ENST00000190611.9	c.870G>A	p.Ser290Ser	synonymous_variant	Exon 10 of 25	1	NM_032523.4	ENSP00000190611.4

Frequencies

GnomAD3 genomes AF: 0.913 AC: 138928 AN: 152166 Hom.: 63477 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.885

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.900

GnomAD3 exomes AF: 0.928 AC: 232437 AN: 250410 Hom.: 107937 AF XY: 0.928 AC XY: 125693 AN XY: 135426

Gnomad AFR exome AF: 0.890

Gnomad AMR exome AF: 0.944

Gnomad ASJ exome AF: 0.907

Gnomad EAS exome AF: 0.967

Gnomad SAS exome AF: 0.952

Gnomad FIN exome AF: 0.946

Gnomad NFE exome AF: 0.915

Gnomad OTH exome AF: 0.922

GnomAD4 exome AF: 0.917 AC: 1338071 AN: 1458592 Hom.: 613998 Cov.: 37 AF XY: 0.918 AC XY: 666454 AN XY: 725754

Gnomad4 AFR exome AF: 0.891

Gnomad4 AMR exome AF: 0.941

Gnomad4 ASJ exome AF: 0.907

Gnomad4 EAS exome AF: 0.973

Gnomad4 SAS exome AF: 0.952

Gnomad4 FIN exome AF: 0.943

Gnomad4 NFE exome AF: 0.912

Gnomad4 OTH exome AF: 0.913

GnomAD4 genome AF: 0.913 AC: 139036 AN: 152286 Hom.: 63527 Cov.: 32 AF XY: 0.916 AC XY: 68169 AN XY: 74458

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.948

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.899

Alfa AF: 0.913 Hom.: 105388

Bravo AF: 0.910

Asia WGS AF: 0.954 AC: 3318 AN: 3478

EpiCase AF: 0.905

EpiControl AF: 0.904

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	9.8
DANN	Benign	0.62

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: rs1434087; hg19: chr2-179203797;