Variant rs2279008 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004145.4(MYO9B):c.1935+16T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,610,968 control chromosomes in the GnomAD database, including 52,018 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 0.23 ( 4430 hom., cov: 31)

Exomes 𝑓: 0.25 ( 47588 hom. )

Consequence

MYO9B
NM_004145.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.249

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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.1935+16T>C		intron_variant		ENST00000682292.1	NP_004136.2
MYO9B	NM_001130065.2 linkuse as main transcript	c.1935+16T>C		intron_variant			NP_001123537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO9B	ENST00000682292.1 linkuse as main transcript	c.1935+16T>C		intron_variant			NM_004145.4	ENSP00000507803	A2	Q13459-1

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34690

AN:

151918

Hom.:

4428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.355

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.252

AC:

61403

AN:

243994

Hom.:

7951

AF XY:

0.250

AC XY:

33145

AN XY:

132418

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.207

Gnomad EAS exome

AF:

0.353

Gnomad SAS exome

AF:

0.210

Gnomad FIN exome

AF:

0.365

Gnomad NFE exome

AF:

0.248

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.252

AC:

367765

AN:

1458932

Hom.:

47588

Cov.:

AF XY:

0.251

AC XY:

182256

AN XY:

725486

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.207

Gnomad4 EAS exome

AF:

0.345

Gnomad4 SAS exome

AF:

0.213

Gnomad4 FIN exome

AF:

0.356

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.228

AC:

34707

AN:

152036

Hom.:

4430

Cov.:

AF XY:

0.235

AC XY:

17495

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.124

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.354

Gnomad4 SAS

AF:

0.212

Gnomad4 FIN

AF:

0.376

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.244

Hom.:

9302

Bravo

AF:

0.217

Asia WGS

AF:

0.251

AC:

875

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.0

DANN

Benign

0.35

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