chr10-117537968-C-T

Variant names:

• chr10-117537968-C-T
• rs242956
• ENST00000551288.5:n.574+6338G>A

Variant summary

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

The ENST00000551288.5(EMX2OS):​n.574+6338G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,178 control chromosomes in the GnomAD database, including 22,418 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 0.52 (22418 hom., cov: 34)
• Consequence: EMX2OS ENST00000551288.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 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+6338G>A		intron	N/A
	EMX2OS	NR_144378.1		n.493+4129G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMX2OS	ENST00000551288.5	TSL:1	n.574+6338G>A		intron	N/A
	EMX2OS	ENST00000440007.7	TSL:2	n.497+4129G>A		intron	N/A
	EMX2OS	ENST00000450314.7	TSL:2	n.431+4129G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79555 AN: 152060 Hom.: 22412 Cov.: 34

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.523 AC: 79587 AN: 152178 Hom.: 22418 Cov.: 34 AF XY: 0.520 AC XY: 38654 AN XY: 74402

African (AFR) AF: 0.309 AC: 12825 AN: 41534

American (AMR) AF: 0.598 AC: 9144 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1920 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2899 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2136 AN: 4828

European-Finnish (FIN) AF: 0.559 AC: 5931 AN: 10608

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42721 AN: 67948

Other (OTH) AF: 0.586 AC: 1237 AN: 2112

Alfa AF: 0.440 Hom.: 1310

Bravo AF: 0.526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.3
DANN	Benign	0.88
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs242956; hg19: chr10-119297479;