Genetic Variant GMEB2:c.*193T>A (chr20-63589896-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_012384.5(GMEB2):c.*193T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000714 in 280,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)

Exomes 𝑓: 0.0000071 ( 0 hom. )

Consequence

GMEB2
NM_012384.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.506

Publications

27 publications found

Variant links:

Genes affected

GMEB2 (HGNC:4371): (glucocorticoid modulatory element binding protein 2) This gene is a member of KDWK gene family. The product of this gene associates with GMEB1 protein, and the complex is essential for parvovirus DNA replication. Study of rat homolog implicates the role of this gene in modulation of transactivation by the glucocorticoid receptor bound to glucocorticoid response elements. This gene appears to use multiple polyadenylation sites. [provided by RefSeq, Jul 2008]

GMEB2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GMEB2	NM_012384.5 link	c.*193T>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000370077.2	NP_036516.1	Q9UKD1B4DQS0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GMEB2	ENST00000370077.2 link	c.*193T>A	3_prime_UTR_variant	Exon 10 of 10	1	NM_012384.5	ENSP00000359094.1	Q9UKD1
GMEB2	ENST00000266068.5 link	c.*193T>A	3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000266068.1	Q9UKD1
GMEB2	ENST00000370069.5 link	c.*193T>A	3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000359086.1	Q5JTV1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000714

AC:

AN:

280092

Hom.:

Cov.:

AF XY:

0.0000139

AC XY:

AN XY:

143480

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

7728

American (AMR)

AF:

0.00

AC:

AN:

8958

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9768

East Asian (EAS)

AF:

0.0000842

AC:

AN:

23748

South Asian (SAS)

AF:

0.00

AC:

AN:

8770

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22976

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1384

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

178852

Other (OTH)

AF:

0.00

AC:

AN:

17908

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.3

(source)

DANN

Benign

0.64

PhyloP100

-0.51

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

20-63589896-A-T

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