rs13438327

Variant names:

• chr7-97991379-G-A
• rs13438327
• ENST00000473987.2:n.-210C>T

Variant summary

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

The ENST00000473987.2(OCM2):​n.-210C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,150 control chromosomes in the GnomAD database, including 893 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 0.10 (893 hom., cov: 32)
• Consequence: OCM2 ENST00000473987.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.844
• Publications: 11 publications found

Genes affected

OCM2 (HGNC:34396): (oncomodulin 2) This gene is similar to the oncomodulin gene, a high-affinity calcium ion-binding protein that belongs to the superfamily of calmodulin proteins, also known as the EF-hand proteins. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OCM2	ENST00000473987.2	n.-210C>T		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15523 AN: 152032 Hom.: 888 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.00848

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.102 AC: 15546 AN: 152150 Hom.: 893 Cov.: 32 AF XY: 0.101 AC XY: 7480 AN XY: 74404

African (AFR) AF: 0.154 AC: 6401 AN: 41494

American (AMR) AF: 0.0806 AC: 1230 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3472

East Asian (EAS) AF: 0.00850 AC: 44 AN: 5176

South Asian (SAS) AF: 0.139 AC: 670 AN: 4814

European-Finnish (FIN) AF: 0.0534 AC: 567 AN: 10612

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5841 AN: 68000

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.0940 Hom.: 2357

Bravo AF: 0.106

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.77
PhyloP100		0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13438327; hg19: chr7-97620691;