10-117541943-C-T

Variant names:

• chr10-117541943-C-T
• rs1638626
• ENST00000551288.5:n.574+2363G>A

Variant summary

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

The ENST00000551288.5(EMX2OS):​n.574+2363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,248 control chromosomes in the GnomAD database, including 1,458 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 0.12 (1458 hom., cov: 33)
• Consequence: EMX2OS ENST00000551288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551288.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	NR_002791.2		n.574+2363G>A		intron	N/A
	EMX2OS	NR_144378.1		n.493+154G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	ENST00000551288.5	TSL:1	n.574+2363G>A		intron	N/A
	EMX2OS	ENST00000440007.7	TSL:2	n.497+154G>A		intron	N/A
	EMX2OS	ENST00000450314.7	TSL:2	n.431+154G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18596 AN: 152130 Hom.: 1455 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 18610 AN: 152248 Hom.: 1458 Cov.: 33 AF XY: 0.125 AC XY: 9269 AN XY: 74446

African (AFR) AF: 0.207 AC: 8611 AN: 41524

American (AMR) AF: 0.109 AC: 1671 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5174

South Asian (SAS) AF: 0.0809 AC: 390 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1289 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0727 AC: 4946 AN: 68026

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0924 Hom.: 1745

Bravo AF: 0.125

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.9
DANN	Benign	0.87
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1638626; hg19: chr10-119301454;