Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001614.5(ACTG1):c.1026T>C(p.Gly342Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 1,612,654 control chromosomes in the GnomAD database, including 637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.041 ( 222 hom., cov: 32)

Exomes 𝑓: 0.017 ( 415 hom. )

Consequence

ACTG1
NM_001614.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -3.01

Publications

12 publications found

Variant links:

Genes affected

ACTG1 (HGNC:144): (actin gamma 1) Actins are highly conserved proteins that are involved in various types of cell motility and in maintenance of the cytoskeleton. Three main groups of actin isoforms have been identified in vertebrate animals: alpha, beta, and gamma. The alpha actins are found in muscle tissues and are a major constituent of the contractile apparatus. The beta and gamma actins co-exist in most cell types as components of the cytoskeleton and as mediators of internal cell motility. Actin gamma 1, encoded by this gene, is a cytoplasmic actin found in all cell types. Mutations in this gene are associated with DFNA20/26, a subtype of autosomal dominant non-syndromic sensorineural progressive hearing loss and also with Baraitser-Winter syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]

ACTG1 Gene-Disease associations (from GenCC):

Baraitser-winter syndrome 2
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
nonsyndromic genetic hearing loss
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
autosomal dominant nonsyndromic hearing loss 20
Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
autosomal dominant nonsyndromic hearing loss
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Baraitser-Winter cerebrofrontofacial syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACTG1 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=-0.83).

BP6

Variant 17-81510792-A-G is Benign according to our data. Variant chr17-81510792-A-G is described in ClinVar as Benign. ClinVar VariationId is 128268.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001614.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ACTG1	NM_001614.5	MANE Select	c.1026T>C	p.Gly342Gly	synonymous	Exon 6 of 6	NP_001605.1
ACTG1	NM_001199954.3		c.1026T>C	p.Gly342Gly	synonymous	Exon 6 of 6	NP_001186883.1
ACTG1	NR_037688.3		n.1098T>C		non_coding_transcript_exon	Exon 6 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ACTG1	ENST00000573283.7	TSL:5 MANE Select	c.1026T>C	p.Gly342Gly	synonymous	Exon 6 of 6	ENSP00000458435.1
ACTG1	ENST00000575842.5	TSL:1	c.1026T>C	p.Gly342Gly	synonymous	Exon 5 of 5	ENSP00000458162.1
ACTG1	ENST00000615544.5	TSL:1	c.1026T>C	p.Gly342Gly	synonymous	Exon 6 of 6	ENSP00000477968.1

Frequencies

GnomAD3 genomes

AF:

0.0405

AC:

6115

AN:

150880

Hom.:

224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.00333

Gnomad AMR

AF:

0.0302

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.0339

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.00548

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0417

GnomAD2 exomes

AF:

0.0225

AC:

5645

AN:

251294

AF XY:

0.0208

show subpopulations

Gnomad AFR exome

AF:

0.0999

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0485

Gnomad EAS exome

AF:

0.0302

Gnomad FIN exome

AF:

0.00638

Gnomad NFE exome

AF:

0.0134

Gnomad OTH exome

AF:

0.0210

GnomAD4 exome

AF:

0.0165

AC:

24137

AN:

1461654

Hom.:

415

Cov.:

AF XY:

0.0163

AC XY:

11845

AN XY:

727138

show subpopulations

African (AFR)

AF:

0.0991

AC:

3319

AN:

33476

American (AMR)

AF:

0.0199

AC:

890

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0499

AC:

1303

AN:

26136

East Asian (EAS)

AF:

0.0223

AC:

885

AN:

39700

South Asian (SAS)

AF:

0.0170

AC:

1470

AN:

86252

European-Finnish (FIN)

AF:

0.00573

AC:

305

AN:

53256

Middle Eastern (MID)

AF:

0.0277

AC:

160

AN:

5768

European-Non Finnish (NFE)

AF:

0.0129

AC:

14375

AN:

1111960

Other (OTH)

AF:

0.0237

AC:

1430

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

1569

3139

4708

6278

7847

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

636

1272

1908

2544

3180

<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:

0.0406

AC:

6124

AN:

151000

Hom.:

222

Cov.:

AF XY:

0.0402

AC XY:

2965

AN XY:

73820

show subpopulations

African (AFR)

AF:

0.101

AC:

4165

AN:

41086

American (AMR)

AF:

0.0302

AC:

460

AN:

15210

Ashkenazi Jewish (ASJ)

AF:

0.0516

AC:

178

AN:

3452

East Asian (EAS)

AF:

0.0338

AC:

171

AN:

5066

South Asian (SAS)

AF:

0.0170

AC:

AN:

4754

European-Finnish (FIN)

AF:

0.00548

AC:

AN:

10588

Middle Eastern (MID)

AF:

0.0137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0136

AC:

917

AN:

67564

Other (OTH)

AF:

0.0417

AC:

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

286

572

859

1145

1431

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0279

Hom.:

Bravo

AF:

0.0439

Asia WGS

AF:

0.0400

AC:

137

AN:

3478

EpiCase

AF:

0.0162

EpiControl

AF:

0.0158

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (4)

not provided (3)

Autosomal dominant nonsyndromic hearing loss 20 (1)

Autosomal dominant nonsyndromic hearing loss 20;C3281235:Baraitser-winter syndrome 2 (1)

Baraitser-winter syndrome 2 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.62

(source)

DANN

Benign

0.51

PhyloP100

-3.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=97/3

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

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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

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over