rs1055419

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-125594988-G-A
• chr3-125594988-G-C
• chr3-125594988-G-T

Variant summary

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

The NM_022776.5(OSBPL11):​c.-188C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 597,580 control chromosomes in the GnomAD database, including 1,305 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 0.074 (588 hom., cov: 32)
  • Exomes 𝑓: 0.050 (717 hom.)
• Consequence: OSBPL11 NM_022776.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL11	NM_022776.5	c.-188C>T		5_prime_UTR_variant	Exon 1 of 13	ENST00000296220.6	NP_073613.2
OSBPL11	XM_047447396.1	c.-188C>T		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>T		5_prime_UTR_variant	Exon 1 of 13	1	NM_022776.5	ENSP00000296220.5

Frequencies

GnomAD3 genomes AF: 0.0744 AC: 11314 AN: 152068 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.0593

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0651

GnomAD4 exome AF: 0.0499 AC: 22229 AN: 445394 Hom.: 717 Cov.: 6 AF XY: 0.0495 AC XY: 11474 AN XY: 231840

African (AFR) AF: 0.156 AC: 1959 AN: 12582

American (AMR) AF: 0.0867 AC: 1546 AN: 17830

Ashkenazi Jewish (ASJ) AF: 0.0365 AC: 473 AN: 12944

East Asian (EAS) AF: 0.0778 AC: 2355 AN: 30278

South Asian (SAS) AF: 0.0573 AC: 2191 AN: 38232

European-Finnish (FIN) AF: 0.0268 AC: 754 AN: 28100

Middle Eastern (MID) AF: 0.0297 AC: 58 AN: 1954

European-Non Finnish (NFE) AF: 0.0415 AC: 11556 AN: 278340

Other (OTH) AF: 0.0532 AC: 1337 AN: 25134

GnomAD4 genome AF: 0.0744 AC: 11330 AN: 152186 Hom.: 588 Cov.: 32 AF XY: 0.0730 AC XY: 5429 AN XY: 74410

African (AFR) AF: 0.149 AC: 6200 AN: 41504

American (AMR) AF: 0.0797 AC: 1218 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.0620 AC: 321 AN: 5180

South Asian (SAS) AF: 0.0589 AC: 284 AN: 4820

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0400 AC: 2718 AN: 68012

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0555 Hom.: 81

Bravo AF: 0.0823

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		-0.72
Mutation Taster		=300/0	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: rs1055419; hg19: chr3-125313832;