rs935431

Variant names:

• chr11-3088067-G-A
• rs935431
• NM_020896.4:c.*138C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-3088067-G-A
• chr11-3088067-G-C

Variant summary

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

The NM_020896.4(OSBPL5):​c.*138C>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 0.107 in 804,802 control chromosomes in the GnomAD database, including 5,417 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 0.096 (808 hom., cov: 34)
  • Exomes 𝑓: 0.11 (4609 hom.)
• Consequence: OSBPL5 NM_020896.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.159 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL5	NM_020896.4	MANE Select	c.*138C>T		3_prime_UTR	Exon 22 of 22	NP_065947.1
	OSBPL5	NM_001144063.2		c.*138C>T		3_prime_UTR	Exon 21 of 21	NP_001137535.1
	OSBPL5	NM_145638.3		c.*138C>T		3_prime_UTR	Exon 21 of 21	NP_663613.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OSBPL5	ENST00000263650.12	TSL:1 MANE Select	c.*138C>T		3_prime_UTR	Exon 22 of 22	ENSP00000263650.7
	OSBPL5	ENST00000389989.7	TSL:1	c.*138C>T		3_prime_UTR	Exon 21 of 21	ENSP00000374639.3
	OSBPL5	ENST00000866647.1		c.*138C>T		3_prime_UTR	Exon 22 of 22	ENSP00000536706.1

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14598 AN: 152108 Hom.: 809 Cov.: 34

Gnomad AFR AF: 0.0573

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.110 AC: 71576 AN: 652576 Hom.: 4609 Cov.: 9 AF XY: 0.108 AC XY: 35220 AN XY: 326490

African (AFR) AF: 0.0602 AC: 876 AN: 14546

American (AMR) AF: 0.159 AC: 1920 AN: 12064

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 1910 AN: 13712

East Asian (EAS) AF: 0.00505 AC: 135 AN: 26714

South Asian (SAS) AF: 0.0510 AC: 1826 AN: 35818

European-Finnish (FIN) AF: 0.0664 AC: 1868 AN: 28132

Middle Eastern (MID) AF: 0.141 AC: 318 AN: 2260

European-Non Finnish (NFE) AF: 0.121 AC: 59193 AN: 487802

Other (OTH) AF: 0.112 AC: 3530 AN: 31528

GnomAD4 genome AF: 0.0959 AC: 14594 AN: 152226 Hom.: 808 Cov.: 34 AF XY: 0.0917 AC XY: 6822 AN XY: 74402

African (AFR) AF: 0.0571 AC: 2373 AN: 41548

American (AMR) AF: 0.165 AC: 2518 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5170

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4824

European-Finnish (FIN) AF: 0.0633 AC: 671 AN: 10596

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7899 AN: 68004

Other (OTH) AF: 0.128 AC: 270 AN: 2112

Alfa AF: 0.0453 Hom.: 34

Bravo AF: 0.104

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.048
DANN	Benign	0.75
PhyloP100		-0.97
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: rs935431; hg19: chr11-3109297; COSMIC: COSV55143149; COSMIC: COSV55143149;