chr11-3087276-G-A

Variant names:

• chr11-3087276-G-A
• rs8813
• NM_020896.4:c.*929C>T

Variant summary

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

The NM_020896.4(OSBPL5):​c.*929C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 153,308 control chromosomes in the GnomAD database, including 2,658 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 0.17 (2640 hom., cov: 34)
  • Exomes 𝑓: 0.18 (18 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 13 publications found

Genes affected

OSBPL5 (HGNC:16392): (oxysterol binding protein like 5) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors that play a key role in the maintenance of cholesterol balance in the body. Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. This gene has been shown to be imprinted, with preferential expression from the maternal allele only in placenta. Transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020896.4. 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
	OSBPL5	NM_020896.4	MANE Select	c.*929C>T		3_prime_UTR	Exon 22 of 22	NP_065947.1
	OSBPL5	NM_001144063.2		c.*929C>T		3_prime_UTR	Exon 21 of 21	NP_001137535.1
	OSBPL5	NM_145638.3		c.*929C>T		3_prime_UTR	Exon 21 of 21	NP_663613.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL5	ENST00000263650.12	TSL:1 MANE Select	c.*929C>T		3_prime_UTR	Exon 22 of 22	ENSP00000263650.7
	OSBPL5	ENST00000389989.7	TSL:1	c.*929C>T		3_prime_UTR	Exon 21 of 21	ENSP00000374639.3
	OSBPL5	ENST00000478260.5	TSL:2	c.*929C>T		3_prime_UTR	Exon 8 of 8	ENSP00000437141.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25127 AN: 152100 Hom.: 2639 Cov.: 34

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.183 AC: 199 AN: 1090 Hom.: 18 Cov.: 0 AF XY: 0.186 AC XY: 110 AN XY: 590

African (AFR) AF: 0.0357 AC: 1 AN: 28

American (AMR) AF: 0.125 AC: 1 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.158 AC: 6 AN: 38

European-Finnish (FIN) AF: 0.228 AC: 61 AN: 268

Middle Eastern (MID) AF: 0.178 AC: 75 AN: 422

European-Non Finnish (NFE) AF: 0.181 AC: 46 AN: 254

Other (OTH) AF: 0.132 AC: 9 AN: 68

GnomAD4 genome AF: 0.165 AC: 25126 AN: 152218 Hom.: 2640 Cov.: 34 AF XY: 0.163 AC XY: 12147 AN XY: 74418

African (AFR) AF: 0.0564 AC: 2344 AN: 41552

American (AMR) AF: 0.133 AC: 2033 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.00463 AC: 24 AN: 5180

South Asian (SAS) AF: 0.131 AC: 632 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2577 AN: 10590

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16172 AN: 67990

Other (OTH) AF: 0.151 AC: 318 AN: 2110

Alfa AF: 0.213 Hom.: 3283

Bravo AF: 0.151

Asia WGS AF: 0.0630 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		1.5
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: rs8813; hg19: chr11-3108506; COSMIC: COSV55147099; COSMIC: COSV55147099;