18-24358420-T-C

Position:

• chr18-24358420-T-C

Variant summary

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

The ENST00000399441.4(OSBPL1A):​c.*71A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 700,632 control chromosomes in the GnomAD database, including 120,320 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 0.62 (30069 hom., cov: 33)
  • Exomes 𝑓: 0.56 (90251 hom.)
• Consequence: OSBPL1A ENST00000399441.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OSBPL1A	NM_080597.4	c.282+8472A>G		intron_variant		ENST00000319481.8
LOC124904267	XR_007066312.1	n.327-1572T>C		intron_variant, non_coding_transcript_variant
OSBPL1A	XM_017025530.2	c.336+8472A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OSBPL1A	ENST00000319481.8	c.282+8472A>G		intron_variant		1	NM_080597.4	P1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93559 AN: 152014 Hom.: 30022 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.602

GnomAD4 exome AF: 0.564 AC: 309578 AN: 548500 Hom.: 90251 Cov.: 0 AF XY: 0.562 AC XY: 166927 AN XY: 296978

Gnomad4 AFR exome AF: 0.784

Gnomad4 AMR exome AF: 0.714

Gnomad4 ASJ exome AF: 0.513

Gnomad4 EAS exome AF: 0.809

Gnomad4 SAS exome AF: 0.589

Gnomad4 FIN exome AF: 0.532

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.569

GnomAD4 genome AF: 0.616 AC: 93664 AN: 152132 Hom.: 30069 Cov.: 33 AF XY: 0.617 AC XY: 45883 AN XY: 74370

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.596

Alfa AF: 0.546 Hom.: 12737

Bravo AF: 0.637

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.57

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: rs7226913; hg19: chr18-21938384;