2-174221387-C-T

Variant names:

• chr2-174221387-C-T
• rs9332424
• NM_013341.5:c.373+1646G>A

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+1646G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,916 control chromosomes in the GnomAD database, including 19,336 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 0.49 (19336 hom., cov: 31)
• Consequence: OLA1 NM_013341.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLA1	NM_013341.5	c.373+1646G>A		intron_variant	Intron 4 of 10	ENST00000284719.8	NP_037473.3
OLA1	NM_001328688.2	c.373+1646G>A		intron_variant	Intron 4 of 10		NP_001315617.1
OLA1	NM_001011708.3	c.-102+1646G>A		intron_variant	Intron 3 of 9		NP_001011708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLA1	ENST00000284719.8	c.373+1646G>A		intron_variant	Intron 4 of 10	1	NM_013341.5	ENSP00000284719.3
OLA1	ENST00000428402.6	c.373+1646G>A		intron_variant	Intron 4 of 7	1		ENSP00000410385.2
OLA1	ENST00000409546.5	c.433+1646G>A		intron_variant	Intron 4 of 10	5		ENSP00000386350.1
OLA1	ENST00000344357.9	c.-102+1646G>A		intron_variant	Intron 3 of 9	2		ENSP00000340167.5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75002 AN: 151798 Hom.: 19308 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.494 AC: 75085 AN: 151916 Hom.: 19336 Cov.: 31 AF XY: 0.502 AC XY: 37265 AN XY: 74236

African (AFR) AF: 0.434 AC: 17971 AN: 41428

American (AMR) AF: 0.503 AC: 7670 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1918 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5117 AN: 5178

South Asian (SAS) AF: 0.709 AC: 3411 AN: 4808

European-Finnish (FIN) AF: 0.493 AC: 5193 AN: 10526

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32072 AN: 67936

Other (OTH) AF: 0.536 AC: 1132 AN: 2112

Alfa AF: 0.485 Hom.: 13453

Bravo AF: 0.492

Asia WGS AF: 0.785 AC: 2728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.43
PhyloP100		-0.026
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: rs9332424; hg19: chr2-175086115;