Variant rs12145360 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152372.4(MYOM3):c.3197T>C(p.Ile1066Thr) variant causes a missense change. The variant allele was found at a frequency of 0.143 in 1,613,636 control chromosomes in the GnomAD database, including 18,275 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.16 ( 2163 hom., cov: 31)

Exomes 𝑓: 0.14 ( 16112 hom. )

Consequence

MYOM3
NM_152372.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.83

Variant links:

Genes affected

MYOM3 (HGNC:26679): (myomesin 3) Predicted to enable actin filament binding activity and protein homodimerization activity. Predicted to be involved in muscle contraction. Predicted to be active in M band. [provided by Alliance of Genome Resources, Apr 2022]

MYOM3 links:

MYOM3-AS1 (HGNC:41158): (MYOM3 antisense RNA 1)

MYOM3-AS1 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016693771).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOM3	NM_152372.4 linkuse as main transcript	c.3197T>C	p.Ile1066Thr	missense_variant	26/37	ENST00000374434.4	NP_689585.3
MYOM3-AS1	XR_001737930.2 linkuse as main transcript	n.81+1479A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYOM3	ENST00000374434.4 linkuse as main transcript	c.3197T>C	p.Ile1066Thr	missense_variant	26/37	1	NM_152372.4	ENSP00000363557	P1	Q5VTT5-1
MYOM3-AS1	ENST00000429191.1 linkuse as main transcript	n.69+1479A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000439239.2 linkuse as main transcript	n.404+4048A>G		intron_variant, non_coding_transcript_variant		5
MYOM3	ENST00000448831.1 linkuse as main transcript	n.188-11995T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24629

AN:

151942

Hom.:

2166

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.292

Gnomad EAS

AF:

0.204

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.163

AC:

40797

AN:

249524

Hom.:

3750

AF XY:

0.168

AC XY:

22805

AN XY:

135380

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.302

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.245

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.174

GnomAD4 exome

AF:

0.141

AC:

205575

AN:

1461576

Hom.:

16112

Cov.:

AF XY:

0.144

AC XY:

105004

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.139

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.178

Gnomad4 SAS exome

AF:

0.246

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.166

GnomAD4 genome

AF:

0.162

AC:

24646

AN:

152060

Hom.:

2163

Cov.:

AF XY:

0.165

AC XY:

12248

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.198

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.292

Gnomad4 EAS

AF:

0.205

Gnomad4 SAS

AF:

0.247

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.151

Hom.:

3236

Bravo

AF:

0.166

TwinsUK

AF:

0.125

AC:

463

ALSPAC

AF:

0.128

AC:

493

ESP6500AA

AF:

0.178

AC:

715

ESP6500EA

AF:

0.134

AC:

1118

ExAC

AF:

0.164

AC:

19763

Asia WGS

AF:

0.233

AC:

810

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.30

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.050

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.010

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.69

MetaRNN

Benign

0.0017

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.77

MutationTaster

Benign

0.050

P;P;P

PrimateAI

Uncertain

0.58

PROVEAN

Benign

-2.2

REVEL

Benign

0.063

Sift

Benign

0.28

Sift4G

Benign

0.10

Polyphen

0.016

Vest4

0.059

MPC

0.13

ClinPred

0.012

GERP RS

4.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.078

gMVP

0.61

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over