NM_080597.4:c.282+8198A>C

Variant names:

• chr18-24358694-T-G
• rs7227401
• NM_080597.4:c.282+8198A>C

Variant summary

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

The NM_080597.4(OSBPL1A):​c.282+8198A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,046 control chromosomes in the GnomAD database, including 36,791 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 0.69 (36791 hom., cov: 32)
• Consequence: OSBPL1A NM_080597.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 15 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]

LOC124904267 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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.282+8198A>C		intron	N/A	NP_542164.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL1A	ENST00000319481.8	TSL:1 MANE Select	c.282+8198A>C		intron	N/A	ENSP00000320291.3
	OSBPL1A	ENST00000399441.4	TSL:1	c.283-183A>C		intron	N/A	ENSP00000382370.4
	OSBPL1A	ENST00000578091.5	TSL:5	n.127+9673A>C		intron	N/A	ENSP00000462887.1

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104484 AN: 151928 Hom.: 36745 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.688 AC: 104587 AN: 152046 Hom.: 36791 Cov.: 32 AF XY: 0.686 AC XY: 51000 AN XY: 74300

African (AFR) AF: 0.834 AC: 34620 AN: 41508

American (AMR) AF: 0.708 AC: 10813 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1990 AN: 3466

East Asian (EAS) AF: 0.843 AC: 4360 AN: 5172

South Asian (SAS) AF: 0.621 AC: 2989 AN: 4812

European-Finnish (FIN) AF: 0.621 AC: 6549 AN: 10546

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41168 AN: 67964

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.638 Hom.: 96356

Bravo AF: 0.705

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.82
PhyloP100		-0.27
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: rs7227401; hg19: chr18-21938658;