10-117534610-C-T

Variant names:

• chr10-117534610-C-T
• rs1860399
• ENST00000551288.5:n.574+9696G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000551288.5(EMX2OS):​n.574+9696G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,164 control chromosomes in the GnomAD database, including 8,287 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 0.32 (8287 hom., cov: 33)
• Consequence: EMX2OS ENST00000551288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 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+9696G>A		intron	N/A
	EMX2OS	NR_144378.1		n.493+7487G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	ENST00000551288.5	TSL:1	n.574+9696G>A		intron	N/A
	EMX2OS	ENST00000440007.7	TSL:2	n.497+7487G>A		intron	N/A
	EMX2OS	ENST00000450314.7	TSL:2	n.431+7487G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49070 AN: 152044 Hom.: 8283 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.323 AC: 49099 AN: 152164 Hom.: 8287 Cov.: 33 AF XY: 0.328 AC XY: 24406 AN XY: 74384

African (AFR) AF: 0.402 AC: 16693 AN: 41508

American (AMR) AF: 0.309 AC: 4724 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1785 AN: 5146

South Asian (SAS) AF: 0.435 AC: 2098 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3606 AN: 10604

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18061 AN: 68002

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.286 Hom.: 5389

Bravo AF: 0.317

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Benign	0.89
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1860399;

hg19: chr10-119294121;