Genetic Variant ENAH:p.Gly346Arg (chr1-225514778-C-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

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

The NM_018212.6(ENAH):c.1036G>A(p.Gly346Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000226 in 884,964 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G346W) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000034 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000012 ( 0 hom. )

Consequence

ENAH
NM_018212.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.57

Publications

0 publications found

Variant links:

Genes affected

ENAH (HGNC:18271): (ENAH actin regulator) This gene encodes a member of the enabled/ vasodilator-stimulated phosphoprotein. Members of this gene family are involved in actin-based motility. This protein is involved in regulating the assembly of actin filaments and modulates cell adhesion and motility. Alternate splice variants of this gene have been correlated with tumor invasiveness in certain tissues and these variants may serve as prognostic markers. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Sep 2016]

ENAH links:

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ACMG classification

Classification was made for transcript

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
ENAH	NM_018212.6 link	c.1036G>A	p.Gly346Arg	missense_variant	Exon 7 of 14	ENST00000366843.7	NP_060682.2	Q8N8S7-2A0A4D6J698

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENAH	ENST00000366843.7 link	c.1036G>A	p.Gly346Arg	missense_variant	Exon 7 of 14	1	NM_018212.6	ENSP00000355808.2		Q8N8S7-2

Frequencies

GnomAD3 genomes

AF:

0.0000337

AC:

AN:

29672

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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

GnomAD4 exome

AF:

0.00000117

AC:

AN:

855292

Hom.:

Cov.:

AF XY:

0.00000241

AC XY:

AN XY:

415158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

16670

American (AMR)

AF:

0.00

AC:

AN:

15060

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11158

East Asian (EAS)

AF:

0.00

AC:

AN:

8630

South Asian (SAS)

AF:

0.0000292

AC:

AN:

34276

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22744

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1976

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

715150

Other (OTH)

AF:

0.00

AC:

AN:

29628

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000337

AC:

AN:

29672

Hom.:

Cov.:

AF XY:

0.0000718

AC XY:

AN XY:

13930

show subpopulations

African (AFR)

AF:

0.000145

AC:

AN:

6890

American (AMR)

AF:

0.00

AC:

AN:

2226

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

776

East Asian (EAS)

AF:

0.00

AC:

AN:

948

South Asian (SAS)

AF:

0.00

AC:

AN:

960

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1318

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

15882

Other (OTH)

AF:

0.00

AC:

AN:

428

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.61

BayesDel_addAF

Uncertain

0.086

BayesDel_noAF

Benign

-0.11

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.50

D;.;.

Eigen

Uncertain

0.52

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.76

T;D;D

M_CAP

Uncertain

0.16

MetaRNN

Uncertain

0.56

D;D;D

MetaSVM

Uncertain

0.59

MutationAssessor

Uncertain

2.7

M;.;M

PhyloP100

4.6

PrimateAI

Pathogenic

0.83

PROVEAN

Uncertain

-4.0

D;.;D

REVEL

Benign

0.26

Sift

Uncertain

0.0020

D;.;D

Sift4G

Uncertain

0.0020

D;D;D

Polyphen

1.0

D;.;D

Vest4

0.72

MutPred

0.17

Loss of relative solvent accessibility (P = 0.0404);.;Loss of relative solvent accessibility (P = 0.0404);

MVP

0.46

MPC

1.0

ClinPred

0.98

GERP RS

4.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.52

gMVP

0.19

Mutation Taster

=19/81

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over