Genetic Variant MYNN:c.1399+56G>A (chr3-169782699-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018657.5(MYNN):c.1399+56G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,455,106 control chromosomes in the GnomAD database, including 52,129 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 0.21 ( 4457 hom., cov: 32)

Exomes 𝑓: 0.26 ( 47672 hom. )

Consequence

MYNN
NM_018657.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148

Publications

43 publications found

Variant links:

Genes affected

MYNN (HGNC:14955): (myoneurin) This gene encodes a member of the BTB/POZ and zinc finger domain-containing protein family that are involved in the control of gene expression. Alternative splicing results in multiple transcript variants and a pseudogene has been identified on chromosome 14. [provided by RefSeq, Jun 2010]

MYNN links:

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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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018657.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYNN	NM_018657.5	MANE Select	c.1399+56G>A	intron	N/A	NP_061127.1	Q9NPC7-1
MYNN	NM_001185118.2		c.1399+56G>A	intron	N/A	NP_001172047.1	Q9NPC7-1
MYNN	NM_001185119.1		c.1399+56G>A	intron	N/A	NP_001172048.1	Q9NPC7-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYNN	ENST00000349841.10	TSL:1 MANE Select	c.1399+56G>A	intron	N/A	ENSP00000326240.4	Q9NPC7-1
MYNN	ENST00000356716.8	TSL:1	c.1399+56G>A	intron	N/A	ENSP00000349150.3	Q9NPC7-1
MYNN	ENST00000544106.5	TSL:1	c.1399+56G>A	intron	N/A	ENSP00000440637.1	Q9NPC7-2

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32325

AN:

151972

Hom.:

4453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0649

Gnomad AMI

AF:

0.0967

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.565

Gnomad SAS

AF:

0.259

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.228

GnomAD4 exome

AF:

0.258

AC:

336655

AN:

1303016

Hom.:

47672

AF XY:

0.259

AC XY:

169021

AN XY:

652212

show subpopulations

African (AFR)

AF:

0.0521

AC:

1466

AN:

28154

American (AMR)

AF:

0.432

AC:

12901

AN:

29842

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

4288

AN:

23392

East Asian (EAS)

AF:

0.611

AC:

23171

AN:

37940

South Asian (SAS)

AF:

0.269

AC:

19367

AN:

71974

European-Finnish (FIN)

AF:

0.273

AC:

12953

AN:

47456

Middle Eastern (MID)

AF:

0.252

AC:

1294

AN:

5132

European-Non Finnish (NFE)

AF:

0.246

AC:

247511

AN:

1004530

Other (OTH)

AF:

0.251

AC:

13704

AN:

54596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

11501

23002

34502

46003

57504

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8346

16692

25038

33384

41730

<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:

0.213

AC:

32331

AN:

152090

Hom.:

4457

Cov.:

AF XY:

0.218

AC XY:

16217

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0648

AC:

2690

AN:

41512

American (AMR)

AF:

0.316

AC:

4824

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

609

AN:

3470

East Asian (EAS)

AF:

0.565

AC:

2925

AN:

5178

South Asian (SAS)

AF:

0.260

AC:

1253

AN:

4822

European-Finnish (FIN)

AF:

0.264

AC:

2799

AN:

10584

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16603

AN:

67932

Other (OTH)

AF:

0.226

AC:

477

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1245

2490

3735

4980

6225

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.153

Hom.:

413

Bravo

AF:

0.214

Asia WGS

AF:

0.370

AC:

1286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

-0.15

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

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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

Computational scores

Splicing

Publications

Other links and lift over