rs11083021

chr18-24218886-G-Achr18-24218886-G-Cchr18-24218886-G-T

Variant summary

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

The NM_080597.4(OSBPL1A):c.1601+6156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,228 control chromosomes in the GnomAD database, including 61,587 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 0.90 (61587 hom., cov: 32)
• Consequence: OSBPL1A NM_080597.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

OSBPL1A (HGNC:16398): (oxysterol binding protein like 1A) 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, although some members contain only the sterol-binding domain. Transcript variants derived from alternative promoter usage and/or alternative splicing exist; they encode different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL1A	NM_080597.4	c.1601+6156C>T		intron_variant		ENST00000319481.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL1A	ENST00000319481.8	c.1601+6156C>T		intron_variant		1	NM_080597.4	P1

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136691 AN: 152110 Hom.: 61538 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.926

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.899 AC: 136801 AN: 152228 Hom.: 61587 Cov.: 32 AF XY: 0.898 AC XY: 66854 AN XY: 74422

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.899

Alfa AF: 0.907 Hom.: 12711

Bravo AF: 0.900

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.57
Dann	Benign	0.43

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: rs11083021; hg19: chr18-21798850;