rs2286629

Positions:

• chr10-117542183-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450314.6(EMX2OS):​n.137A>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 ENST00000450314.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMX2OS	NR_002791.2	n.574+2123A>C		intron_variant, non_coding_transcript_variant
EMX2OS	NR_144378.1	n.407A>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMX2OS	ENST00000450314.6	n.137A>C		non_coding_transcript_exon_variant	1/3	2

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

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.0588

Gnomad4 NFE exome AF: 0.161

Gnomad4 OTH exome AF: 0.192

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.154

Alfa AF: 0.174 Hom.: 301

Bravo AF: 0.171

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.29
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286629; hg19: chr10-119301694;