chr2-174221387-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_013341.5(OLA1):​c.373+1646G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLA1	NM_013341.5	c.373+1646G>T		intron_variant	Intron 4 of 10	ENST00000284719.8	NP_037473.3
OLA1	NM_001328688.2	c.373+1646G>T		intron_variant	Intron 4 of 10		NP_001315617.1
OLA1	NM_001011708.3	c.-102+1646G>T		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>T		intron_variant	Intron 4 of 10	1	NM_013341.5	ENSP00000284719.3
OLA1	ENST00000428402.6	c.373+1646G>T		intron_variant	Intron 4 of 7	1		ENSP00000410385.2
OLA1	ENST00000409546.5	c.433+1646G>T		intron_variant	Intron 4 of 10	5		ENSP00000386350.1
OLA1	ENST00000344357.9	c.-102+1646G>T		intron_variant	Intron 3 of 9	2		ENSP00000340167.5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		-0.026
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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;