10-117541943-C-T

Position:

• chr10-117541943-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+2363G>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 0.122 in 152,248 control chromosomes in the GnomAD database, including 1,458 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 0.12 (1458 hom., cov: 33)
• Consequence: EMX2OS NR_002791.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMX2OS	NR_002791.2	n.574+2363G>A		intron_variant, non_coding_transcript_variant
EMX2OS	NR_144378.1	n.493+154G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMX2OS	ENST00000450314.6	n.223+154G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18596 AN: 152130 Hom.: 1455 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.122 AC: 18610 AN: 152248 Hom.: 1458 Cov.: 33 AF XY: 0.125 AC XY: 9269 AN XY: 74446

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0809

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0800 Hom.: 799

Bravo AF: 0.125

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1638626; hg19: chr10-119301454;