Genetic Variant NM_033054.3:c.1482C>T (chr7-44969726-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_033054.3(MYO1G):c.1482C>T(p.His494His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,610,064 control chromosomes in the GnomAD database, including 133,975 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 0.38 ( 11211 hom., cov: 32)

Exomes 𝑓: 0.41 ( 122764 hom. )

Consequence

MYO1G
NM_033054.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.316

Publications

13 publications found

Variant links:

Genes affected

MYO1G (HGNC:13880): (myosin IG) MYO1G is a plasma membrane-associated class I myosin (see MIM 601478) that is abundant in T and B lymphocytes and mast cells (Pierce et al., 2001 [PubMed 11544309]; Patino-Lopez et al., 2010 [PubMed 20071333]).[supplied by OMIM, Jun 2010]

MYO1G links:

ENSG00000308366 (HGNC:):

ENSG00000308366 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=0.316 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1G	NM_033054.3 link	c.1482C>T	p.His494His	synonymous_variant	Exon 11 of 22	ENST00000258787.12	NP_149043.2	B0I1T2-1
MYO1G	XR_007060129.1 link	n.1536C>T		non_coding_transcript_exon_variant	Exon 11 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1G	ENST00000258787.12 link	c.1482C>T	p.His494His	synonymous_variant	Exon 11 of 22	1	NM_033054.3	ENSP00000258787.7		B0I1T2-1

Frequencies

GnomAD3 genomes

AF:

0.381

AC:

57701

AN:

151568

Hom.:

11202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.460

Gnomad EAS

AF:

0.616

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.402

Gnomad OTH

AF:

0.413

GnomAD2 exomes

AF:

0.407

AC:

101626

AN:

249390

AF XY:

0.410

show subpopulations

Gnomad AFR exome

AF:

0.315

Gnomad AMR exome

AF:

0.362

Gnomad ASJ exome

AF:

0.471

Gnomad EAS exome

AF:

0.610

Gnomad FIN exome

AF:

0.357

Gnomad NFE exome

AF:

0.405

Gnomad OTH exome

AF:

0.403

GnomAD4 exome

AF:

0.408

AC:

594391

AN:

1458376

Hom.:

122764

Cov.:

AF XY:

0.409

AC XY:

296762

AN XY:

725488

show subpopulations

African (AFR)

AF:

0.306

AC:

10237

AN:

33410

American (AMR)

AF:

0.367

AC:

16387

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

12239

AN:

26078

East Asian (EAS)

AF:

0.652

AC:

25848

AN:

39652

South Asian (SAS)

AF:

0.413

AC:

35540

AN:

86076

European-Finnish (FIN)

AF:

0.364

AC:

19096

AN:

52400

Middle Eastern (MID)

AF:

0.463

AC:

2100

AN:

4540

European-Non Finnish (NFE)

AF:

0.403

AC:

447727

AN:

1111336

Other (OTH)

AF:

0.419

AC:

25217

AN:

60198

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

20317

40634

60950

81267

101584

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14006

28012

42018

56024

70030

<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:

0.381

AC:

57749

AN:

151688

Hom.:

11211

Cov.:

AF XY:

0.380

AC XY:

28197

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.313

AC:

12945

AN:

41412

American (AMR)

AF:

0.378

AC:

5761

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.460

AC:

1591

AN:

3462

East Asian (EAS)

AF:

0.617

AC:

3156

AN:

5118

South Asian (SAS)

AF:

0.408

AC:

1964

AN:

4818

European-Finnish (FIN)

AF:

0.354

AC:

3743

AN:

10584

Middle Eastern (MID)

AF:

0.483

AC:

140

AN:

290

European-Non Finnish (NFE)

AF:

0.402

AC:

27240

AN:

67750

Other (OTH)

AF:

0.417

AC:

876

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1801

3602

5402

7203

9004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.387

Hom.:

4736

Bravo

AF:

0.383

Asia WGS

AF:

0.487

AC:

1693

AN:

3478

EpiCase

AF:

0.406

EpiControl

AF:

0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

7.5

(source)

DANN

Benign

0.32

PhyloP100

0.32

Mutation Taster

=74/26

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over