Variant chr3-169786467-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018657.5(MYNN):c.1622A>G(p.Gln541Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,461,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

MYNN
NM_018657.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.06

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 made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.041719824).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYNN	NM_018657.5 linkuse as main transcript	c.1622A>G	p.Gln541Arg	missense_variant	8/8	ENST00000349841.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYNN	ENST00000349841.10 linkuse as main transcript	c.1622A>G	p.Gln541Arg	missense_variant	8/8	1	NM_018657.5	P1	Q9NPC7-1
MYNN	ENST00000356716.8 linkuse as main transcript	c.1622A>G	p.Gln541Arg	missense_variant	9/9	1		P1	Q9NPC7-1
MYNN	ENST00000544106.5 linkuse as main transcript	c.1535A>G	p.Gln512Arg	missense_variant	6/6	1			Q9NPC7-2
MYNN	ENST00000602751.5 linkuse as main transcript	c.*1230A>G		3_prime_UTR_variant, NMD_transcript_variant	8/8	1			Q9NPC7-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000717

AC:

AN:

250980

Hom.:

AF XY:

0.0000664

AC XY:

AN XY:

135628

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000521

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000164

AC:

AN:

1461462

Hom.:

Cov.:

AF XY:

0.0000193

AC XY:

AN XY:

727018

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000492

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000264

ExAC

AF:

0.0000659

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 30, 2022

The c.1622A>G (p.Q541R) alteration is located in exon 9 (coding exon 7) of the MYNN gene. This alteration results from a A to G substitution at nucleotide position 1622, causing the glutamine (Q) at amino acid position 541 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.63

CADD

Benign

DANN

Uncertain

0.97

DEOGEN2

Benign

0.012

T;T;.

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.0088

FATHMM_MKL

Uncertain

0.91

M_CAP

Benign

0.0036

MetaRNN

Benign

0.042

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

N;N;.

MutationTaster

Benign

0.76

N;N;N

PrimateAI

Benign

0.46

PROVEAN

Benign

-0.55

N;N;N

REVEL

Benign

0.081

Sift

Benign

0.10

T;T;T

Sift4G

Benign

0.48

T;T;T

Polyphen

0.85

P;P;B

Vest4

0.089

MutPred

0.14

Loss of methylation at K546 (P = 0.0775);Loss of methylation at K546 (P = 0.0775);.;

MVP

0.40

MPC

0.35

ClinPred

0.028

GERP RS

4.1

Varity_R

0.034

gMVP

0.32

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

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