rs2884471

chr2-174185614-A-Gchr2-174185614-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

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
OLA1	NM_013341.5	c.373+37419T>C		intron_variant		ENST00000284719.8
LOC124907906	XR_007087307.1	n.29127T>C		non_coding_transcript_exon_variant	2/2
OLA1	NM_001011708.3	c.-102+37419T>C		intron_variant
OLA1	NM_001328688.2	c.373+37419T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OLA1	ENST00000284719.8	c.373+37419T>C		intron_variant		1	NM_013341.5	P1

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

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

Other links and lift over

dbSNP: rs2884471; hg19: chr2-175050342;