10-117494227-C-T

Variant names:

• chr10-117494227-C-T
• rs11198013
• ENST00000551288.5:n.575-2118G>A

Variant summary

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

The ENST00000551288.5(EMX2OS):​n.575-2118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,140 control chromosomes in the GnomAD database, including 2,338 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 0.15 (2338 hom., cov: 32)
• Consequence: EMX2OS ENST00000551288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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.575-2118G>A		intron	N/A
	EMX2OS	NR_144378.1		n.494-2118G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	ENST00000551288.5	TSL:1	n.575-2118G>A		intron	N/A
	EMX2OS	ENST00000423419.1	TSL:3	n.120+342G>A		intron	N/A
	EMX2OS	ENST00000440007.7	TSL:2	n.498-2118G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23423 AN: 152022 Hom.: 2322 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.154 AC: 23481 AN: 152140 Hom.: 2338 Cov.: 32 AF XY: 0.149 AC XY: 11070 AN XY: 74374

African (AFR) AF: 0.287 AC: 11896 AN: 41482

American (AMR) AF: 0.0942 AC: 1439 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5172

South Asian (SAS) AF: 0.111 AC: 535 AN: 4822

European-Finnish (FIN) AF: 0.0708 AC: 751 AN: 10608

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7936 AN: 67982

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.132 Hom.: 1334

Bravo AF: 0.161

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.27
PhyloP100		0.29

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: rs11198013;

hg19: chr10-119253738;