rs1316981

Variant names:

• chr1-51569386-T-C
• rs1316981
• NM_001416292.1:c.-323-4607T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001416292.1(OSBPL9):​c.-323-4607T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,064 control chromosomes in the GnomAD database, including 5,191 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 0.24 (5191 hom., cov: 32)
• Consequence: OSBPL9 NM_001416292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

OSBPL9 (HGNC:16386): (oxysterol binding protein like 9) 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. This family member functions as a cholesterol transfer protein that regulates Golgi structure and function. Multiple transcript variants, most of which encode distinct isoforms, have been identified. Related pseudogenes have been identified on chromosomes 3, 11 and 12. [provided by RefSeq, Jul 2010]

CALR4P (HGNC:35456): (calreticulin 4, pseudogene)

EPS15-AS1 (HGNC:40219): (EPS15 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OSBPL9	NM_001416292.1	c.-323-4607T>C		intron_variant	Intron 1 of 25		NP_001403221.1
OSBPL9	NM_001416293.1	c.-323-4607T>C		intron_variant	Intron 2 of 26		NP_001403222.1
OSBPL9	NM_001416294.1	c.-438-4607T>C		intron_variant	Intron 2 of 27		NP_001403223.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALR4P	ENST00000431943.1	n.336+162A>G		intron_variant	Intron 3 of 6	6
CALR4P	ENST00000641070.1	n.598+162A>G		intron_variant	Intron 3 of 3
CALR4P	ENST00000641201.1	n.709+162A>G		intron_variant	Intron 4 of 5
CALR4P	ENST00000641477.1	n.680+162A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36189 AN: 151944 Hom.: 5189 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.238 AC: 36186 AN: 152064 Hom.: 5191 Cov.: 32 AF XY: 0.233 AC XY: 17317 AN XY: 74332

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.0305

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.287

Alfa AF: 0.314 Hom.: 8705

Bravo AF: 0.230

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1316981; hg19: chr1-52035058;