Variant chr3-169774313-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_018657.5(MYNN):c.18C>T(p.His6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 1,613,072 control chromosomes in the GnomAD database, including 58,494 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.21 ( 4476 hom., cov: 32)

Exomes 𝑓: 0.26 ( 54018 hom. )

Consequence

MYNN
NM_018657.5 synonymous

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: 3.15

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP7

Synonymous conserved (PhyloP=3.15 with no splicing effect.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYNN	NM_018657.5 linkuse as main transcript	c.18C>T	p.His6=	synonymous_variant	2/8	ENST00000349841.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYNN	ENST00000349841.10 linkuse as main transcript	c.18C>T	p.His6=	synonymous_variant	2/8	1	NM_018657.5	P1	Q9NPC7-1
MYNN	ENST00000356716.8 linkuse as main transcript	c.18C>T	p.His6=	synonymous_variant	3/9	1		P1	Q9NPC7-1
MYNN	ENST00000544106.5 linkuse as main transcript	c.18C>T	p.His6=	synonymous_variant	1/6	1			Q9NPC7-2
MYNN	ENST00000602751.5 linkuse as main transcript	c.18C>T	p.His6=	synonymous_variant, NMD_transcript_variant	2/8	1			Q9NPC7-4

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32419

AN:

152062

Hom.:

4473

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0657

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.565

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.227

GnomAD3 exomes

AF:

0.291

AC:

73225

AN:

251364

Hom.:

12996

AF XY:

0.284

AC XY:

38637

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.0578

Gnomad AMR exome

AF:

0.473

Gnomad ASJ exome

AF:

0.181

Gnomad EAS exome

AF:

0.561

Gnomad SAS exome

AF:

0.275

Gnomad FIN exome

AF:

0.269

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.259

AC:

378152

AN:

1460892

Hom.:

54018

Cov.:

AF XY:

0.260

AC XY:

188774

AN XY:

726786

show subpopulations

Gnomad4 AFR exome

AF:

0.0531

Gnomad4 AMR exome

AF:

0.456

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.274

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.213

AC:

32425

AN:

152180

Hom.:

4476

Cov.:

AF XY:

0.218

AC XY:

16244

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0657

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.176

Gnomad4 EAS

AF:

0.565

Gnomad4 SAS

AF:

0.269

Gnomad4 FIN

AF:

0.264

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.243

Hom.:

10450

Bravo

AF:

0.215

Asia WGS

AF:

0.372

AC:

1293

AN:

3478

EpiCase

AF:

0.242

EpiControl

AF:

0.239

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Chronic osteomyelitis

Other:1

association, no assertion criteria provided

case-control

Department of Orthopeadics and Traumatology, Nanfang Hospital

Sep 01, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.81

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over