Variant 19-17102182-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004145.4(MYO9B):c.465C>T(p.Pro155=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 1,613,702 control chromosomes in the GnomAD database, including 25,463 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 0.14 ( 1750 hom., cov: 32)

Exomes 𝑓: 0.17 ( 23713 hom. )

Consequence

MYO9B
NM_004145.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.56

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=-2.56 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO9B	NM_004145.4 linkuse as main transcript	c.465C>T	p.Pro155=	synonymous_variant	2/40	ENST00000682292.1	NP_004136.2
MYO9B	NM_001130065.2 linkuse as main transcript	c.465C>T	p.Pro155=	synonymous_variant	2/40		NP_001123537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO9B	ENST00000682292.1 linkuse as main transcript	c.465C>T	p.Pro155=	synonymous_variant	2/40		NM_004145.4	ENSP00000507803	A2	Q13459-1

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21112

AN:

152064

Hom.:

1745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0600

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.0203

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.141

AC:

34997

AN:

248980

Hom.:

2853

AF XY:

0.143

AC XY:

19285

AN XY:

135118

show subpopulations

Gnomad AFR exome

AF:

0.0557

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.0977

Gnomad EAS exome

AF:

0.0193

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.161

Gnomad NFE exome

AF:

0.186

Gnomad OTH exome

AF:

0.147

GnomAD4 exome

AF:

0.174

AC:

254407

AN:

1461520

Hom.:

23713

Cov.:

AF XY:

0.173

AC XY:

125550

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.0531

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.0199

Gnomad4 SAS exome

AF:

0.116

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.193

Gnomad4 OTH exome

AF:

0.153

GnomAD4 genome

AF:

0.139

AC:

21136

AN:

152182

Hom.:

1750

Cov.:

AF XY:

0.137

AC XY:

10201

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0604

Gnomad4 AMR

AF:

0.139

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.0203

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.172

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.171

Hom.:

4891

Bravo

AF:

0.131

Asia WGS

AF:

0.0650

AC:

229

AN:

3478

EpiCase

AF:

0.178

EpiControl

AF:

0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.2

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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