GeneBe

rs2884471

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0730
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OLA1NM_013341.5 linkuse as main transcriptc.373+37419T>C intron_variant ENST00000284719.8
LOC124907906XR_007087307.1 linkuse as main transcriptn.29127T>C non_coding_transcript_exon_variant 2/2
OLA1NM_001011708.3 linkuse as main transcriptc.-102+37419T>C intron_variant
OLA1NM_001328688.2 linkuse as main transcriptc.373+37419T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OLA1ENST00000284719.8 linkuse as main transcriptc.373+37419T>C intron_variant 1 NM_013341.5 P1Q9NTK5-1

Frequencies

GnomAD3 genomes
AF:
0.532
AC:
80793
AN:
151870
Hom.:
22075
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.575
Gnomad4 AMR
AF:
0.515
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.945
Gnomad4 SAS
AF:
0.688
Gnomad4 FIN
AF:
0.482
Gnomad4 NFE
AF:
0.474
Gnomad4 OTH
AF:
0.551
Alfa
AF:
0.486
Hom.:
2198
Bravo
AF:
0.536
Asia WGS
AF:
0.760
AC:
2641
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
4.5
DANN
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2884471; hg19: chr2-175050342; API