EBLN1 p.Gly149Arg

Variant names:

• chr10-22209539-C-G
• NM_001394757.1:c.445G>C
• EBLN1 p.Gly149Arg

Your query was ambiguous. Multiple possible variants found:

• chr10-22209539-C-G
• chr10-22209539-C-T
• chr10-22209537-TCC-ACG
• chr10-22209537-TCC-GCG
• chr10-22209537-TCC-CCG
• chr10-22209537-TCC-CCT

Variant summary

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

The NM_001394757.1(EBLN1):​c.445G>C​(p.Gly149Arg) 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. 11/14 in silico tools predict 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: 32)
• Consequence: EBLN1 NM_001394757.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 0 publications found

Genes affected

EBLN1 (HGNC:39430): (endogenous Bornavirus like nucleoprotein 1)

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=0.1043804).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394757.1. 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
	EBLN1	NM_001394757.1	MANE Select	c.445G>C	p.Gly149Arg	missense	Exon 3 of 3	NP_001381686.1	P0CF75
	EBLN1	NM_001199938.2		c.445G>C	p.Gly149Arg	missense	Exon 1 of 1	NP_001186867.1	P0CF75

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBLN1	ENST00000422359.3	TSL:6 MANE Select	c.445G>C	p.Gly149Arg	missense	Exon 3 of 3	ENSP00000473842.1	P0CF75
	EBLN1	ENST00000939589.1		c.445G>C	p.Gly149Arg	missense	Exon 2 of 2	ENSP00000609648.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.032	T
BayesDel_noAF	Benign	-0.28
CADD	Benign	5.8
DANN	Benign	0.50
DEOGEN2	Benign	0.083	T
FATHMM_MKL	Benign	0.0044	N
LIST_S2	Benign	0.52	T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.10	T
MutationAssessor	Benign	0.90	L
PhyloP100		0.010
PrimateAI	Benign	0.38	T
Sift4G	Benign	0.19	T
Varity_R		0.095
gMVP		0.16
Mutation Taster		=100/0	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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr10-22498468;