GeneBe

ENST00000551288.5:n.574+2363G>A

Variant names:

Variant summary

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

The ENST00000551288.5(EMX2OS):​n.574+2363G>A variant causes a intron 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
ENST00000551288.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.409

Publications

2 publications found
Variant links:
Genes affected
EMX2OS (HGNC:18511): (EMX2 opposite strand/antisense RNA)

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=-0.67).
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 rank MANE Protein UniProt
EMX2OSNR_002791.2 linkn.574+2363G>A intron_variant Intron 2 of 3
EMX2OSNR_144378.1 linkn.493+154G>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EMX2OSENST00000551288.5 linkn.574+2363G>A intron_variant Intron 2 of 3 1
EMX2OSENST00000440007.7 linkn.497+154G>A intron_variant Intron 1 of 2 2
EMX2OSENST00000450314.7 linkn.431+154G>A intron_variant Intron 1 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.122
AC:
18596
AN:
152130
Hom.:
1455
Cov.:
33
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.207
AC:
8611
AN:
41524
American (AMR)
AF:
0.109
AC:
1671
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.0619
AC:
215
AN:
3472
East Asian (EAS)
AF:
0.232
AC:
1200
AN:
5174
South Asian (SAS)
AF:
0.0809
AC:
390
AN:
4822
European-Finnish (FIN)
AF:
0.122
AC:
1289
AN:
10606
Middle Eastern (MID)
AF:
0.0646
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
0.0727
AC:
4946
AN:
68026
Other (OTH)
AF:
0.118
AC:
250
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
807
1613
2420
3226
4033
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
196
392
588
784
980
<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:
0.0924
Hom.:
1745
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
PhyloP100
-0.41

Splicing

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

Publications

Other links and lift over

dbSNP: rs1638626; hg19: chr10-119301454; API