rs7227401

Positions:

• chr18-24358694-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL1A	NM_080597.4	c.282+8198A>C		intron_variant		ENST00000319481.8
LOC124904267	XR_007066312.1	n.327-1298T>G		intron_variant, non_coding_transcript_variant
OSBPL1A	XM_017025530.2	c.336+8198A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL1A	ENST00000319481.8	c.282+8198A>C		intron_variant		1	NM_080597.4	P1

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

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.671

Alfa AF: 0.628 Hom.: 36926

Bravo AF: 0.705

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.82

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: rs7227401; hg19: chr18-21938658;