19-17203024-G-A

Variant names:

• chr19-17203024-G-A
• rs2305764
• NM_004145.4:c.4879-123G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_004145.4(MYO9B):​c.4879-123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 1,359,810 control chromosomes in the GnomAD database, including 139,241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.50 (20312 hom., cov: 33)
  • Exomes 𝑓: 0.43 (118929 hom.)
• Consequence: MYO9B NM_004145.4 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.49
• Publications: 39 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 19-17203024-G-A is Benign according to our data. Variant chr19-17203024-G-A is described in ClinVar as Benign. ClinVar VariationId is 7521.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO9B	NM_004145.4	MANE Select	c.4879-123G>A		intron	N/A	NP_004136.2
	MYO9B	NM_001130065.2		c.4879-123G>A		intron	N/A	NP_001123537.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO9B	ENST00000682292.1	MANE Select	c.4879-123G>A		intron	N/A	ENSP00000507803.1
	MYO9B	ENST00000595618.5	TSL:1	c.4879-123G>A		intron	N/A	ENSP00000471457.1
	MYO9B	ENST00000593533.1	TSL:1	n.828+141G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76413 AN: 151932 Hom.: 20292 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.498

GnomAD2 exomes AF: 0.522 AC: 71446 AN: 136978 AF XY: 0.515

Gnomad AFR exome AF: 0.626

Gnomad AMR exome AF: 0.701

Gnomad ASJ exome AF: 0.343

Gnomad EAS exome AF: 0.770

Gnomad FIN exome AF: 0.440

Gnomad NFE exome AF: 0.405

Gnomad OTH exome AF: 0.477

GnomAD4 exome AF: 0.433 AC: 522502 AN: 1207760 Hom.: 118929 Cov.: 17 AF XY: 0.436 AC XY: 259308 AN XY: 595052

African (AFR) AF: 0.630 AC: 17475 AN: 27730

American (AMR) AF: 0.690 AC: 23394 AN: 33928

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 7307 AN: 21916

East Asian (EAS) AF: 0.751 AC: 25685 AN: 34222

South Asian (SAS) AF: 0.566 AC: 40138 AN: 70878

European-Finnish (FIN) AF: 0.433 AC: 20806 AN: 48062

Middle Eastern (MID) AF: 0.469 AC: 2452 AN: 5232

European-Non Finnish (NFE) AF: 0.396 AC: 362047 AN: 914710

Other (OTH) AF: 0.454 AC: 23198 AN: 51082

GnomAD4 genome AF: 0.503 AC: 76483 AN: 152050 Hom.: 20312 Cov.: 33 AF XY: 0.508 AC XY: 37737 AN XY: 74312

African (AFR) AF: 0.622 AC: 25791 AN: 41490

American (AMR) AF: 0.597 AC: 9121 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1177 AN: 3470

East Asian (EAS) AF: 0.763 AC: 3936 AN: 5158

South Asian (SAS) AF: 0.598 AC: 2881 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4765 AN: 10566

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27307 AN: 67948

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.444 Hom.: 28472

Bravo AF: 0.524

Asia WGS AF: 0.638 AC: 2217 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Celiac disease, susceptibility to, 4 Benign:1

Dec 01, 2005

OMIM

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		-2.5
RBP_binding_hub_radar		1.1
RBP_regulation_power_radar		2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2305764; hg19: chr19-17313833;