10-117541071-C-T

Position:

• chr10-117541071-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+3235G>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 0.12 in 152,114 control chromosomes in the GnomAD database, including 1,417 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 (1417 hom., cov: 32)
• Consequence: EMX2OS NR_002791.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMX2OS	NR_002791.2	n.574+3235G>A		intron_variant, non_coding_transcript_variant
EMX2OS	NR_144378.1	n.493+1026G>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+1026G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18201 AN: 151996 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.120 AC: 18212 AN: 152114 Hom.: 1417 Cov.: 32 AF XY: 0.122 AC XY: 9077 AN XY: 74364

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.0888

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.117

Alfa AF: 0.102 Hom.: 242

Bravo AF: 0.120

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703411; hg19: chr10-119300582;