Genetic Variant REST:p.Glu743Glu (chr4-56931087-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_005612.5(REST):c.2229G>A(p.Glu743Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000574 in 1,383,968 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0010 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00053 ( 10 hom. )

Consequence

REST
NM_005612.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.525

Publications

5 publications found

Variant links:

Genes affected

REST (HGNC:9966): (RE1 silencing transcription factor) This gene was initially identified as a transcriptional repressor that represses neuronal genes in non-neuronal tissues. However, depending on the cellular context, this gene can act as either an oncogene or a tumor suppressor. The encoded protein is a member of the Kruppel-type zinc finger transcription factor family. It represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element. The protein is also found in undifferentiated neuronal progenitor cells and it is thought that this repressor may act as a master negative regulator of neurogenesis. Alternatively spliced transcript variants have been described. [provided by RefSeq, May 2018]

REST Gene-Disease associations (from GenCC):

fibromatosis, gingival, 5
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
Wilms tumor 6
Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
hereditary gingival fibromatosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
autosomal dominant nonsyndromic hearing loss 27
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

REST links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 4-56931087-G-A is Benign according to our data. Variant chr4-56931087-G-A is described in ClinVar as Benign. ClinVar VariationId is 789137.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.525 with no splicing effect.

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000996 (130/130570) while in subpopulation EAS AF = 0.0207 (94/4544). AF 95% confidence interval is 0.0173. There are 1 homozygotes in GnomAd4. There are 71 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 130 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005612.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
REST	NM_005612.5	MANE Select	c.2229G>A	p.Glu743Glu	synonymous	Exon 4 of 4	NP_005603.3
REST	NM_001193508.2		c.2229G>A	p.Glu743Glu	synonymous	Exon 4 of 4	NP_001180437.1
REST	NM_001363453.3		c.2229G>A	p.Glu743Glu	synonymous	Exon 4 of 4	NP_001350382.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
REST	ENST00000309042.12	TSL:1 MANE Select	c.2229G>A	p.Glu743Glu	synonymous	Exon 4 of 4	ENSP00000311816.7
REST	ENST00000514063.2	TSL:1	c.*1256G>A		3_prime_UTR	Exon 5 of 5	ENSP00000501649.1
REST	ENST00000619101.5	TSL:1	c.*1256G>A		3_prime_UTR	Exon 5 of 5	ENSP00000484836.2

Frequencies

GnomAD3 genomes

AF:

0.000996

AC:

130

AN:

130492

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000349

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000296

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0206

Gnomad SAS

AF:

0.00152

Gnomad FIN

AF:

0.000338

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000154

Gnomad OTH

AF:

0.000539

GnomAD2 exomes

AF:

0.000847

AC:

210

AN:

247856

AF XY:

0.000888

show subpopulations

Gnomad AFR exome

AF:

0.000126

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0108

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000448

Gnomad OTH exome

AF:

0.000494

GnomAD4 exome

AF:

0.000530

AC:

664

AN:

1253398

Hom.:

Cov.:

AF XY:

0.000563

AC XY:

353

AN XY:

626608

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

27672

American (AMR)

AF:

0.00

AC:

AN:

41174

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23326

East Asian (EAS)

AF:

0.0163

AC:

545

AN:

33528

South Asian (SAS)

AF:

0.000519

AC:

AN:

82778

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45050

Middle Eastern (MID)

AF:

0.000186

AC:

AN:

5384

European-Non Finnish (NFE)

AF:

0.0000573

AC:

AN:

942212

Other (OTH)

AF:

0.000402

AC:

AN:

52274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

128

170

213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.000996

AC:

130

AN:

130570

Hom.:

Cov.:

AF XY:

0.00111

AC XY:

AN XY:

63916

show subpopulations

African (AFR)

AF:

0.000348

AC:

AN:

34520

American (AMR)

AF:

0.000295

AC:

AN:

13538

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3094

East Asian (EAS)

AF:

0.0207

AC:

AN:

4544

South Asian (SAS)

AF:

0.00152

AC:

AN:

4600

European-Finnish (FIN)

AF:

0.000338

AC:

AN:

8868

Middle Eastern (MID)

AF:

0.00

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.000154

AC:

AN:

58586

Other (OTH)

AF:

0.000539

AC:

AN:

1856

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

Alfa

AF:

0.0413

Hom.:

EpiCase

AF:

0.000218

EpiControl

AF:

0.0000594

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Jan 22, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.36

(source)

DANN

Benign

0.34

PhyloP100

-0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over