Genetic Variant EMX2OS:n.574+2123A>C (chr10-117542183-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000551288.5(EMX2OS):n.574+2123A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,784 control chromosomes in the GnomAD database, including 2,732 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 0.18 ( 2720 hom., cov: 34)

Exomes 𝑓: 0.16 ( 12 hom. )

Consequence

EMX2OS
ENST00000551288.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

2 publications found

Variant links:

Genes affected

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

EMX2OS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EMX2OS	NR_144378.1 link	n.407A>C		non_coding_transcript_exon_variant	Exon 1 of 3
EMX2OS	NR_002791.2 link	n.574+2123A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EMX2OS	ENST00000551288.5 link	n.574+2123A>C	intron_variant	Intron 2 of 3	1
EMX2OS	ENST00000440007.7 link	n.411A>C	non_coding_transcript_exon_variant	Exon 1 of 3	2
EMX2OS	ENST00000450314.7 link	n.345A>C	non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27446

AN:

152042

Hom.:

2717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.345

Gnomad FIN

AF:

0.217

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.156

GnomAD4 exome

AF:

0.161

AC:

101

AN:

626

Hom.:

Cov.:

AF XY:

0.159

AC XY:

AN XY:

472

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.286

AC:

AN:

European-Finnish (FIN)

AF:

0.0588

AC:

AN:

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.161

AC:

AN:

508

Other (OTH)

AF:

0.192

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.180

AC:

27452

AN:

152158

Hom.:

2720

Cov.:

AF XY:

0.185

AC XY:

13772

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.132

AC:

5482

AN:

41556

American (AMR)

AF:

0.205

AC:

3143

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

820

AN:

3470

East Asian (EAS)

AF:

0.144

AC:

742

AN:

5146

South Asian (SAS)

AF:

0.345

AC:

1662

AN:

4820

European-Finnish (FIN)

AF:

0.217

AC:

2299

AN:

10588

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.187

AC:

12717

AN:

67962

Other (OTH)

AF:

0.154

AC:

325

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1189

2379

3568

4758

5947

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.173

Hom.:

309

Bravo

AF:

0.171

Asia WGS

AF:

0.232

AC:

808

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.29

(source)

DANN

Benign

0.38

PhyloP100

-1.5

PromoterAI

0.039

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over