rs782262879

Variant names:

• chr12-6916497-C-G
• rs782262879
• NM_001975.3:c.166C>G

Your query was ambiguous. Multiple possible variants found:

• chr12-6916497-C-G
• chr12-6916497-C-T

Variant summary

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

The NM_001975.3(ENO2):​c.166C>G​(p.Arg56Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R56C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ENO2 NM_001975.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.11
• Publications: 0 publications found

Genes affected

ENO2 (HGNC:3353): (enolase 2) This gene encodes one of the three enolase isoenzymes found in mammals. This isoenzyme, a homodimer, is found in mature neurons and cells of neuronal origin. A switch from alpha enolase to gamma enolase occurs in neural tissue during development in rats and primates. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENO2	NM_001975.3	c.166C>G	p.Arg56Gly	missense_variant	Exon 3 of 12	ENST00000229277.6	NP_001966.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENO2	ENST00000229277.6	c.166C>G	p.Arg56Gly	missense_variant	Exon 3 of 12	1	NM_001975.3	ENSP00000229277.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Pathogenic	0.26	D
BayesDel_noAF	Uncertain	0.13
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T;T;T;.;.;T
Eigen	Uncertain	0.51
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.89	D;.;D;D;D;.
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.57	D;D;D;D;D;D
MetaSVM	Benign	-0.60	T
MutationAssessor	Pathogenic	4.0	.;H;H;H;.;H
PhyloP100		4.1
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-3.5	D;N;N;N;N;N
REVEL	Uncertain	0.41
Sift	Benign	0.034	D;D;D;D;T;D
Sift4G	Uncertain	0.0060	D;D;D;D;D;D
Polyphen		0.59	.;P;P;.;.;P
Vest4		0.91, 0.92, 0.91
MutPred		0.51		Gain of ubiquitination at K60 (P = 0.0417);Gain of ubiquitination at K60 (P = 0.0417);Gain of ubiquitination at K60 (P = 0.0417);Gain of ubiquitination at K60 (P = 0.0417);Gain of ubiquitination at K60 (P = 0.0417);Gain of ubiquitination at K60 (P = 0.0417);
MVP		0.61
MPC		1.4
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.79
gMVP		0.90

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: rs782262879; hg19: chr12-7025661;