1-28714238-C-A

Variant names:

• chr1-28714238-C-A
• rs753788875
• NM_001319674.2:c.1157C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001319674.2(GMEB1):​c.1157C>A​(p.Pro386His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GMEB1 NM_001319674.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.50
• Publications: 2 publications found

Genes affected

GMEB1 (HGNC:4370): (glucocorticoid modulatory element binding protein 1) This gene encodes a member of KDWK gene family which associates with GMEB2 protein. The GMEB1-GMEB2 complex is essential for parvovirus DNA replication. Studies in rat for a similar gene suggest that this gene's role is to modulate the transactivation of the glucocorticoid receptor when it is bound to glucocorticoid response elements. Three alternative spliced transcript variants encoding different isoforms exist. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24464831).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001319674.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GMEB1	NM_001319674.2	MANE Select	c.1157C>A	p.Pro386His	missense	Exon 10 of 10	NP_001306603.1	Q9Y692-2
	GMEB1	NM_006582.4		c.1187C>A	p.Pro396His	missense	Exon 10 of 10	NP_006573.2
	GMEB1	NM_024482.3		c.1157C>A	p.Pro386His	missense	Exon 10 of 10	NP_077808.1	Q9Y692-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GMEB1	ENST00000373816.6	TSL:2 MANE Select	c.1157C>A	p.Pro386His	missense	Exon 10 of 10	ENSP00000362922.1	Q9Y692-2
	GMEB1	ENST00000294409.2	TSL:1	c.1187C>A	p.Pro396His	missense	Exon 10 of 10	ENSP00000294409.2	Q9Y692-1
	GMEB1	ENST00000361872.8	TSL:1	c.1157C>A	p.Pro386His	missense	Exon 10 of 10	ENSP00000355186.4	Q9Y692-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.044	T
BayesDel_noAF	Benign	-0.30
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.023	T
Eigen	Uncertain	0.64
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.84	T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.24	T
MetaSVM	Benign	-0.75	T
MutationAssessor	Benign	1.6	L
PhyloP100		3.5
PrimateAI	Uncertain	0.57	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.15
Sift	Benign	0.49	T
Sift4G	Uncertain	0.032	D
Polyphen		1.0	D
Vest4		0.37
MutPred		0.18		Loss of glycosylation at P396 (P = 0.0167)
MVP		0.28
MPC		0.89
ClinPred		0.89	D
GERP RS		5.9
Varity_R		0.14
gMVP		0.30
Mutation Taster		=78/22	polymorphism

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

Other links and lift over

dbSNP: rs753788875; hg19: chr1-29040750;