rs242967

Variant names:

• chr10-117473864-A-G
• rs242967
• ENST00000412075.6:n.818-442T>C

Variant summary

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

The ENST00000412075.6(EMX2OS):​n.818-442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,930 control chromosomes in the GnomAD database, including 34,592 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 0.67 (34592 hom., cov: 30)
• Consequence: EMX2OS ENST00000412075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 4 publications found

Genes affected

EMX2OS (HGNC:18511): (EMX2 opposite strand/antisense RNA)

ENSG00000258114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 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
EMX2OS	ENST00000412075.6	n.818-442T>C		intron_variant	Intron 1 of 1	2
EMX2OS	ENST00000424371.2	n.277-442T>C		intron_variant	Intron 1 of 1	2
EMX2OS	ENST00000450314.7	n.521-442T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101395 AN: 151812 Hom.: 34534 Cov.: 30

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.668 AC: 101511 AN: 151930 Hom.: 34592 Cov.: 30 AF XY: 0.670 AC XY: 49764 AN XY: 74226

African (AFR) AF: 0.796 AC: 33005 AN: 41438

American (AMR) AF: 0.595 AC: 9090 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2233 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3185 AN: 5158

South Asian (SAS) AF: 0.805 AC: 3877 AN: 4814

European-Finnish (FIN) AF: 0.623 AC: 6543 AN: 10508

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41575 AN: 67962

Other (OTH) AF: 0.653 AC: 1373 AN: 2104

Alfa AF: 0.620 Hom.: 45892

Bravo AF: 0.665

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.81
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs242967; hg19: chr10-119233375;