Genetic Variant MTA3:c.*700A>G (chr2-42754099-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001330442.2(MTA3):c.*700A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 985,122 control chromosomes in the GnomAD database, including 55,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.35 ( 9325 hom., cov: 32)

Exomes 𝑓: 0.33 ( 46043 hom. )

Consequence

MTA3
NM_001330442.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336

Publications

17 publications found

Variant links:

Genes affected

MTA3 (HGNC:23784): (metastasis associated 1 family member 3) Predicted to enable histone deacetylase binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of NuRD complex. [provided by Alliance of Genome Resources, Apr 2022]

MTA3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330442.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTA3	NM_001330442.2	MANE Select	c.*700A>G	3_prime_UTR	Exon 17 of 17	NP_001317371.1
MTA3	NM_001330443.2		c.*700A>G	3_prime_UTR	Exon 17 of 17	NP_001317372.1
MTA3	NM_001282755.2		c.*700A>G	3_prime_UTR	Exon 18 of 18	NP_001269684.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MTA3	ENST00000405094.2	TSL:5 MANE Select	c.*700A>G	3_prime_UTR	Exon 17 of 17	ENSP00000385823.1
MTA3	ENST00000406652.5	TSL:1	c.*700A>G	3_prime_UTR	Exon 17 of 17	ENSP00000384249.1
MTA3	ENST00000405592.5	TSL:2	c.*700A>G	3_prime_UTR	Exon 18 of 18	ENSP00000383973.1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52589

AN:

151864

Hom.:

9328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.412

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.349

GnomAD4 exome

AF:

0.332

AC:

276398

AN:

833136

Hom.:

46043

Cov.:

AF XY:

0.332

AC XY:

127761

AN XY:

384738

show subpopulations

African (AFR)

AF:

0.404

AC:

6381

AN:

15786

American (AMR)

AF:

0.444

AC:

437

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

2032

AN:

5152

East Asian (EAS)

AF:

0.181

AC:

658

AN:

3630

South Asian (SAS)

AF:

0.365

AC:

6005

AN:

16464

European-Finnish (FIN)

AF:

0.248

AC:

AN:

278

Middle Eastern (MID)

AF:

0.465

AC:

753

AN:

1620

European-Non Finnish (NFE)

AF:

0.329

AC:

250686

AN:

761924

Other (OTH)

AF:

0.344

AC:

9377

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

10745

21489

32234

42978

53723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11170

22340

33510

44680

55850

<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:

0.346

AC:

52616

AN:

151986

Hom.:

9325

Cov.:

AF XY:

0.344

AC XY:

25560

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.396

AC:

16387

AN:

41432

American (AMR)

AF:

0.412

AC:

6288

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1375

AN:

3464

East Asian (EAS)

AF:

0.191

AC:

985

AN:

5158

South Asian (SAS)

AF:

0.365

AC:

1755

AN:

4804

European-Finnish (FIN)

AF:

0.234

AC:

2470

AN:

10578

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.327

AC:

22222

AN:

67970

Other (OTH)

AF:

0.345

AC:

729

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1773

3546

5320

7093

8866

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.333

Hom.:

18582

Bravo

AF:

0.362

Asia WGS

AF:

0.290

AC:

1007

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.4

(source)

DANN

Benign

0.72

PhyloP100

-0.34

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Computational scores

Splicing

Publications

Other links and lift over