chr19-17200417-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004145.4(MYO9B):c.4363G>A(p.Gly1455Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 1,578,960 control chromosomes in the GnomAD database, including 1,187 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 81 hom., cov: 32)

Exomes 𝑓: 0.038 ( 1106 hom. )

Consequence

MYO9B
NM_004145.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.721

Publications

8 publications found

Variant links:

Genes affected

MYO9B (HGNC:7609): (myosin IXB) This gene encodes a member of the myosin family of actin-based molecular motor heavy chain proteins. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-9 (MYH9). The protein has four IQ motifs located in the neck domain that bind calmodulin, which serves as a light chain. The protein complex has a single-headed structure and exhibits processive movement on actin filaments toward the minus-end. The protein also has rho-GTPase activity. Polymorphisms in this gene are associated with celiac disease and ulcerative colitis susceptibility. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

MYO9B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018480718).

BP6

Variant 19-17200417-G-A is Benign according to our data. Variant chr19-17200417-G-A is described in ClinVar as Benign. ClinVar VariationId is 403217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0277 (4216/152304) while in subpopulation NFE AF = 0.0438 (2981/68018). AF 95% confidence interval is 0.0425. There are 81 homozygotes in GnomAd4. There are 1971 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 4216 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004145.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO9B	NM_004145.4	MANE Select	c.4363G>A	p.Gly1455Ser	missense	Exon 25 of 40	NP_004136.2
	MYO9B	NM_001130065.2		c.4363G>A	p.Gly1455Ser	missense	Exon 25 of 40	NP_001123537.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
MYO9B	ENST00000682292.1	MANE Select	c.4363G>A	p.Gly1455Ser	missense	Exon 25 of 40	ENSP00000507803.1
MYO9B	ENST00000595618.5	TSL:1	c.4363G>A	p.Gly1455Ser	missense	Exon 25 of 40	ENSP00000471457.1
MYO9B	ENST00000593533.1	TSL:1	n.316G>A		non_coding_transcript_exon	Exon 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.0277

AC:

4217

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00702

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.0482

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00662

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0438

Gnomad OTH

AF:

0.0321

GnomAD2 exomes

AF:

0.0297

AC:

5676

AN:

191160

AF XY:

0.0298

show subpopulations

Gnomad AFR exome

AF:

0.00682

Gnomad AMR exome

AF:

0.0197

Gnomad ASJ exome

AF:

0.0447

Gnomad EAS exome

AF:

0.0000732

Gnomad FIN exome

AF:

0.0312

Gnomad NFE exome

AF:

0.0449

Gnomad OTH exome

AF:

0.0341

GnomAD4 exome

AF:

0.0377

AC:

53762

AN:

1426656

Hom.:

1106

Cov.:

AF XY:

0.0369

AC XY:

26111

AN XY:

706718

show subpopulations

African (AFR)

AF:

0.00597

AC:

195

AN:

32672

American (AMR)

AF:

0.0202

AC:

768

AN:

38066

Ashkenazi Jewish (ASJ)

AF:

0.0437

AC:

1118

AN:

25596

East Asian (EAS)

AF:

0.0000786

AC:

AN:

38168

South Asian (SAS)

AF:

0.00927

AC:

763

AN:

82302

European-Finnish (FIN)

AF:

0.0303

AC:

1552

AN:

51228

Middle Eastern (MID)

AF:

0.0203

AC:

113

AN:

5564

European-Non Finnish (NFE)

AF:

0.0434

AC:

47427

AN:

1093926

Other (OTH)

AF:

0.0308

AC:

1823

AN:

59134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

2926

5853

8779

11706

14632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1752

3504

5256

7008

8760

<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:

0.0277

AC:

4216

AN:

152304

Hom.:

Cov.:

AF XY:

0.0265

AC XY:

1971

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.00700

AC:

291

AN:

41578

American (AMR)

AF:

0.0219

AC:

335

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0482

AC:

167

AN:

3468

East Asian (EAS)

AF:

0.000386

AC:

AN:

5184

South Asian (SAS)

AF:

0.00662

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0299

AC:

317

AN:

10614

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0438

AC:

2981

AN:

68018

Other (OTH)

AF:

0.0313

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

206

413

619

826

1032

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0376

Hom.:

398

Bravo

AF:

0.0263

TwinsUK

AF:

0.0364

AC:

135

ALSPAC

AF:

0.0389

AC:

150

ESP6500AA

AF:

0.00713

AC:

ESP6500EA

AF:

0.0397

AC:

332

ExAC

AF:

0.0244

AC:

2915

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.38

DEOGEN2

Benign

0.014

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.010

LIST_S2

Benign

0.61

MetaRNN

Benign

0.0018

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.20

PhyloP100

0.72

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.21

REVEL

Benign

0.15

Sift

Benign

0.76

Sift4G

Benign

0.85

Polyphen

0.0

Vest4

0.082

MPC

0.32

ClinPred

0.000055

GERP RS

-0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

gMVP

0.41

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