rs2119137

Positions:

• chr2-174152986-A-G

Variant summary

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

The NM_013341.5(OLA1):​c.374-10986T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,040 control chromosomes in the GnomAD database, including 7,360 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 0.31 (7360 hom., cov: 32)
• Consequence: OLA1 NM_013341.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

OLA1 (HGNC:28833): (Obg like ATPase 1) This gene encodes a member of the GTPase protein family. The encoded protein interacts with breast cancer-associated gene 1 (BRCA1) and BRCA1-associated RING domain protein (BARD1), and is involved in centrosome regulation. Overexpression of this gene has been observed in multiple types of cancer and may be associated with poor survival. Pseudogenes of this gene have been defined on chromosomes 17 and 22. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OLA1	NM_013341.5	c.374-10986T>C		intron_variant		ENST00000284719.8	NP_037473.3
OLA1	NM_001011708.3	c.-101-10986T>C		intron_variant			NP_001011708.1
OLA1	NM_001328688.2	c.374-10986T>C		intron_variant			NP_001315617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OLA1	ENST00000284719.8	c.374-10986T>C		intron_variant		1	NM_013341.5	ENSP00000284719	P1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46541 AN: 151922 Hom.: 7340 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.307 AC: 46615 AN: 152040 Hom.: 7360 Cov.: 32 AF XY: 0.303 AC XY: 22489 AN XY: 74332

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.335

Alfa AF: 0.336 Hom.: 4125

Bravo AF: 0.302

Asia WGS AF: 0.216 AC: 752 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119137; hg19: chr2-175017714;