rs11198013

Positions:

• chr10-117494227-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.575-2118G>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 0.154 in 152,140 control chromosomes in the GnomAD database, including 2,338 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 0.15 (2338 hom., cov: 32)
• Consequence: EMX2OS NR_002791.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EMX2OS	NR_002791.2	n.575-2118G>A		intron_variant, non_coding_transcript_variant
EMX2OS	NR_144378.1	n.494-2118G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EMX2OS	ENST00000450314.6	n.224-2118G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23423 AN: 152022 Hom.: 2322 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.154 AC: 23481 AN: 152140 Hom.: 2338 Cov.: 32 AF XY: 0.149 AC XY: 11070 AN XY: 74374

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0942

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.0346

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0708

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.133

Alfa AF: 0.133 Hom.: 766

Bravo AF: 0.161

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11198013; hg19: chr10-119253738;