10-117539176-C-T

Position:

• chr10-117539176-C-T

Variant summary

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

The NR_002791.2(EMX2OS):​n.574+5130G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,006 control chromosomes in the GnomAD database, including 7,230 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 0.30 (7230 hom., cov: 33)
• Consequence: EMX2OS NR_002791.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMX2OS	NR_002791.2	n.574+5130G>A		intron_variant, non_coding_transcript_variant
EMX2OS	NR_144378.1	n.493+2921G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMX2OS	ENST00000450314.6	n.223+2921G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45876 AN: 151888 Hom.: 7228 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.302 AC: 45900 AN: 152006 Hom.: 7230 Cov.: 33 AF XY: 0.309 AC XY: 22954 AN XY: 74302

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.274

Alfa AF: 0.275 Hom.: 1315

Bravo AF: 0.292

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0020
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703409; hg19: chr10-119298687;