rs2286629

Variant names:

• chr10-117542183-T-G
• rs2286629
• ENST00000551288.5:n.574+2123A>C

Variant summary

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

The ENST00000440007.7(EMX2OS):​n.411A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,784 control chromosomes in the GnomAD database, including 2,732 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 0.18 (2720 hom., cov: 34)
  • Exomes 𝑓: 0.16 (12 hom.)
• Consequence: EMX2OS ENST00000440007.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440007.7. 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_144378.1		n.407A>C		non_coding_transcript_exon	Exon 1 of 3
	EMX2OS	NR_002791.2		n.574+2123A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	ENST00000551288.5	TSL:1	n.574+2123A>C		intron	N/A
	EMX2OS	ENST00000440007.7	TSL:2	n.411A>C		non_coding_transcript_exon	Exon 1 of 3
	EMX2OS	ENST00000450314.7	TSL:2	n.345A>C		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27446 AN: 152042 Hom.: 2717 Cov.: 34

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.161 AC: 101 AN: 626 Hom.: 12 Cov.: 0 AF XY: 0.159 AC XY: 75 AN XY: 472

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.167 AC: 5 AN: 30

South Asian (SAS) AF: 0.286 AC: 4 AN: 14

European-Finnish (FIN) AF: 0.0588 AC: 2 AN: 34

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.161 AC: 82 AN: 508

Other (OTH) AF: 0.192 AC: 5 AN: 26

GnomAD4 genome AF: 0.180 AC: 27452 AN: 152158 Hom.: 2720 Cov.: 34 AF XY: 0.185 AC XY: 13772 AN XY: 74374

African (AFR) AF: 0.132 AC: 5482 AN: 41556

American (AMR) AF: 0.205 AC: 3143 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.144 AC: 742 AN: 5146

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4820

European-Finnish (FIN) AF: 0.217 AC: 2299 AN: 10588

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12717 AN: 67962

Other (OTH) AF: 0.154 AC: 325 AN: 2116

Alfa AF: 0.173 Hom.: 309

Bravo AF: 0.171

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.29
DANN	Benign	0.38
PhyloP100		-1.5
PromoterAI		0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2286629; hg19: chr10-119301694;