18-24358420-T-C

Variant names:

• chr18-24358420-T-C
• rs7226913
• ENST00000399441.4:c.*71A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399441.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL1A	NM_080597.4	MANE Select	c.282+8472A>G		intron	N/A	NP_542164.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL1A	ENST00000399441.4	TSL:1	c.*71A>G		3_prime_UTR	Exon 5 of 5	ENSP00000382370.4	E7ER58
	OSBPL1A	ENST00000319481.8	TSL:1 MANE Select	c.282+8472A>G		intron	N/A	ENSP00000320291.3	Q9BXW6-1
	OSBPL1A	ENST00000880335.1		c.282+8472A>G		intron	N/A	ENSP00000550394.1

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

African (AFR) AF: 0.784 AC: 12368 AN: 15768

American (AMR) AF: 0.714 AC: 24599 AN: 34464

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 10212 AN: 19896

East Asian (EAS) AF: 0.809 AC: 25981 AN: 32100

South Asian (SAS) AF: 0.589 AC: 36790 AN: 62498

European-Finnish (FIN) AF: 0.532 AC: 17633 AN: 33140

Middle Eastern (MID) AF: 0.559 AC: 2207 AN: 3950

European-Non Finnish (NFE) AF: 0.514 AC: 162417 AN: 316170

Other (OTH) AF: 0.569 AC: 17371 AN: 30514

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

African (AFR) AF: 0.782 AC: 32456 AN: 41498

American (AMR) AF: 0.650 AC: 9934 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4362 AN: 5174

South Asian (SAS) AF: 0.596 AC: 2879 AN: 4832

European-Finnish (FIN) AF: 0.533 AC: 5632 AN: 10576

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34798 AN: 67980

Other (OTH) AF: 0.596 AC: 1262 AN: 2116

Alfa AF: 0.545 Hom.: 13874

Bravo AF: 0.637

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		-0.19
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7226913;

hg19: chr18-21938384;