3-125594988-G-C

Variant names:

• chr3-125594988-G-C
• rs1055419
• NM_022776.5:c.-188C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022776.5(OSBPL11):​c.-188C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000224 in 445,598 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: OSBPL11 NM_022776.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 0 publications found

Genes affected

OSBPL11 (HGNC:16397): (oxysterol binding protein like 11) This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors. Like most members, the encoded protein contains an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL11	NM_022776.5	c.-188C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 13	ENST00000296220.6	NP_073613.2
OSBPL11	NM_022776.5	c.-188C>G		5_prime_UTR_variant	Exon 1 of 13	ENST00000296220.6	NP_073613.2
OSBPL11	XM_047447396.1	c.-188C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 9		XP_047303352.1
OSBPL11	XM_047447396.1	c.-188C>G		5_prime_UTR_variant	Exon 1 of 9		XP_047303352.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OSBPL11	ENST00000296220.6	c.-188C>G		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 13	1	NM_022776.5	ENSP00000296220.5
OSBPL11	ENST00000296220.6	c.-188C>G		5_prime_UTR_variant	Exon 1 of 13	1	NM_022776.5	ENSP00000296220.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000224 AC: 1 AN: 445598 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 231946

African (AFR) AF: 0.0000794 AC: 1 AN: 12594

American (AMR) AF: 0.00 AC: 0 AN: 17842

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12950

East Asian (EAS) AF: 0.00 AC: 0 AN: 30292

South Asian (SAS) AF: 0.00 AC: 0 AN: 38266

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28108

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1954

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 278452

Other (OTH) AF: 0.00 AC: 0 AN: 25140

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.72

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: rs1055419; hg19: chr3-125313832;