chr10-117473864-A-G

Position:

• chr10-117473864-A-G

Variant summary

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

The ENST00000450314.6(EMX2OS):​n.313-442T>C 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 0.668 in 151,930 control chromosomes in the GnomAD database, including 34,592 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 0.67 (34592 hom., cov: 30)
• Consequence: EMX2OS ENST00000450314.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMX2OS	ENST00000450314.6	n.313-442T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000549104.1	n.269-16298A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101395 AN: 151812 Hom.: 34534 Cov.: 30

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.668 AC: 101511 AN: 151930 Hom.: 34592 Cov.: 30 AF XY: 0.670 AC XY: 49764 AN XY: 74226

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.653

Alfa AF: 0.618 Hom.: 38526

Bravo AF: 0.665

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242967; hg19: chr10-119233375;