1-8871910-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7

The NM_001428.5(ENO1):c.162G>A(p.Lys54Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ENO1
NM_001428.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.03

Publications

0 publications found

Variant links:

Genes affected

ENO1 (HGNC:3350): (enolase 1) This gene encodes alpha-enolase, one of three enolase isoenzymes found in mammals. Each isoenzyme is a homodimer composed of 2 alpha, 2 gamma, or 2 beta subunits, and functions as a glycolytic enzyme. Alpha-enolase in addition, functions as a structural lens protein (tau-crystallin) in the monomeric form. Alternative splicing of this gene results in a shorter isoform that has been shown to bind to the c-myc promoter and function as a tumor suppressor. Several pseudogenes have been identified, including one on the long arm of chromosome 1. Alpha-enolase has also been identified as an autoantigen in Hashimoto encephalopathy. [provided by RefSeq, Jan 2011]

ENO1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BP6

Variant 1-8871910-C-T is Benign according to our data. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-8871910-C-T is described in CliVar as Likely_benign. Clinvar id is 731576.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.03 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENO1	NM_001428.5 link	c.162G>A	p.Lys54Lys	synonymous_variant	Exon 3 of 12	ENST00000234590.10	NP_001419.1	P06733-1A0A024R4F1
ENO1	NM_001353346.3 link	c.162G>A	p.Lys54Lys	synonymous_variant	Exon 3 of 12		NP_001340275.1
ENO1	NM_001201483.4 link	c.-1498G>A		5_prime_UTR_variant	Exon 3 of 11		NP_001188412.1	P06733-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENO1	ENST00000234590.10 link	c.162G>A	p.Lys54Lys	synonymous_variant	Exon 3 of 12	1	NM_001428.5	ENSP00000234590.4		P06733-1

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00000795

AC:

AN:

251472

AF XY:

0.0000147

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000879

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000205

AC:

AN:

1461832

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

727214

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33476

American (AMR)

AF:

0.0000224

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86254

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5730

European-Non Finnish (NFE)

AF:

8.99e-7

AC:

AN:

1112004

Other (OTH)

AF:

0.0000166

AC:

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152188

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41452

American (AMR)

AF:

0.000196

AC:

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00

AC:

AN:

4834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68036

Other (OTH)

AF:

0.00

AC:

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000113

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 14, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

(source)

DANN

Benign

0.90

PhyloP100

2.0

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over