Genetic Variant ENST00000551288.5:n.575-2118G>A (chr10-117494227-C-T) – 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.575-2118G>A variant causes a intron 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
ENST00000551288.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.292

Publications

4 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=-0.83).

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 rank	MANE	Protein	UniProt
EMX2OS	NR_002791.2 link	n.575-2118G>A		intron_variant	Intron 2 of 3
EMX2OS	NR_144378.1 link	n.494-2118G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
EMX2OS	ENST00000551288.5 link	n.575-2118G>A	intron_variant	Intron 2 of 3	1
EMX2OS	ENST00000423419.1 link	n.120+342G>A	intron_variant	Intron 1 of 2	3
EMX2OS	ENST00000440007.7 link	n.498-2118G>A	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23423

AN:

152022

Hom.:

2322

Cov.:

show subpopulations

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.:

AF XY:

0.149

AC XY:

11070

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.287

AC:

11896

AN:

41482

American (AMR)

AF:

0.0942

AC:

1439

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0862

AC:

299

AN:

3470

East Asian (EAS)

AF:

0.0346

AC:

179

AN:

5172

South Asian (SAS)

AF:

0.111

AC:

535

AN:

4822

European-Finnish (FIN)

AF:

0.0708

AC:

751

AN:

10608

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7936

AN:

67982

Other (OTH)

AF:

0.133

AC:

281

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

984

1968

2952

3936

4920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.132

Hom.:

1334

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

(source)

DANN

Benign

0.27

PhyloP100

0.29

Splicing

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

Publications

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ENST00000551288.5:n.575-2118G>A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over