19-17146992-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004145.4(MYO9B):c.935+1501T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 152,182 control chromosomes in the GnomAD database, including 18,792 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 0.48 (18792 hom., cov: 33)
• Consequence: MYO9B NM_004145.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO9B	NM_004145.4	c.935+1501T>C		intron_variant		ENST00000682292.1
MYO9B	NM_001130065.2	c.935+1501T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO9B	ENST00000682292.1	c.935+1501T>C		intron_variant			NM_004145.4	A2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72724 AN: 152064 Hom.: 18765 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.438

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.478 AC: 72798 AN: 152182 Hom.: 18792 Cov.: 33 AF XY: 0.478 AC XY: 35540 AN XY: 74380

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.434

Alfa AF: 0.414 Hom.: 7532

Bravo AF: 0.482

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.4
Dann	Benign	0.39

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

Other links and lift over

dbSNP: rs17533945; hg19: chr19-17257802;