rs2884471

Variant names:

• chr2-174185614-A-G
• rs2884471
• NM_013341.5:c.373+37419T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-174185614-A-G
• chr2-174185614-A-T

Variant summary

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

The NM_013341.5(OLA1):​c.373+37419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,988 control chromosomes in the GnomAD database, including 22,103 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 0.53 (22103 hom., cov: 32)
• Consequence: OLA1 NM_013341.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 3 publications found

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]

LOC124907906 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013341.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLA1	NM_013341.5	MANE Select	c.373+37419T>C		intron	N/A	NP_037473.3
	OLA1	NM_001328688.2		c.373+37419T>C		intron	N/A	NP_001315617.1
	OLA1	NM_001011708.3		c.-102+37419T>C		intron	N/A	NP_001011708.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OLA1	ENST00000284719.8	TSL:1 MANE Select	c.373+37419T>C		intron	N/A	ENSP00000284719.3
	OLA1	ENST00000428402.6	TSL:1	c.373+37419T>C		intron	N/A	ENSP00000410385.2
	OLA1	ENST00000409546.5	TSL:5	c.433+37419T>C		intron	N/A	ENSP00000386350.1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80793 AN: 151870 Hom.: 22075 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.532 AC: 80879 AN: 151988 Hom.: 22103 Cov.: 32 AF XY: 0.538 AC XY: 39956 AN XY: 74282

African (AFR) AF: 0.575 AC: 23808 AN: 41410

American (AMR) AF: 0.515 AC: 7872 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1891 AN: 3466

East Asian (EAS) AF: 0.945 AC: 4889 AN: 5176

South Asian (SAS) AF: 0.688 AC: 3313 AN: 4814

European-Finnish (FIN) AF: 0.482 AC: 5089 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32252 AN: 67974

Other (OTH) AF: 0.551 AC: 1163 AN: 2110

Alfa AF: 0.490 Hom.: 2326

Bravo AF: 0.536

Asia WGS AF: 0.760 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.5
DANN	Benign	0.77
PhyloP100		0.073
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: rs2884471; hg19: chr2-175050342;