18-24218886-G-A

Variant names:

• chr18-24218886-G-A
• rs11083021
• NM_080597.4:c.1601+6156C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080597.4. 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
	OSBPL1A	NM_080597.4	MANE Select	c.1601+6156C>T		intron	N/A	NP_542164.2
	OSBPL1A	NM_001242508.1		c.455+6156C>T		intron	N/A	NP_001229437.1
	OSBPL1A	NM_018030.4		c.62+6156C>T		intron	N/A	NP_060500.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL1A	ENST00000319481.8	TSL:1 MANE Select	c.1601+6156C>T		intron	N/A	ENSP00000320291.3
	OSBPL1A	ENST00000399443.7	TSL:1	c.62+6156C>T		intron	N/A	ENSP00000382372.3
	OSBPL1A	ENST00000357041.8	TSL:2	c.455+6156C>T		intron	N/A	ENSP00000349545.4

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

African (AFR) AF: 0.850 AC: 35301 AN: 41518

American (AMR) AF: 0.930 AC: 14221 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3095 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5116 AN: 5186

South Asian (SAS) AF: 0.935 AC: 4509 AN: 4824

European-Finnish (FIN) AF: 0.867 AC: 9185 AN: 10594

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62369 AN: 68030

Other (OTH) AF: 0.899 AC: 1899 AN: 2112

Alfa AF: 0.914 Hom.: 81310

Bravo AF: 0.900

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.43
PhyloP100		-0.83
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: rs11083021; hg19: chr18-21798850;