rs13035033

chr2-170475778-C-G

Variant summary

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

The NM_138995.5(MYO3B):c.3014+9067C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,246 control chromosomes in the GnomAD database, including 3,641 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 0.19 (3641 hom., cov: 33)
• Consequence: MYO3B NM_138995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.958

Genes affected

MYO3B (HGNC:15576): (myosin IIIB) This gene encodes one of the class III myosins. Myosins are ATPases, activated by actin, that move along actin filaments in the cell. This class of myosins are characterized by an amino-terminal kinase domain and shown to be present in photoreceptors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO3B	NM_138995.5	c.3014+9067C>G		intron_variant		ENST00000408978.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO3B	ENST00000408978.9	c.3014+9067C>G		intron_variant		1	NM_138995.5	P1

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29425 AN: 152128 Hom.: 3639 Cov.: 33

Gnomad AFR AF: 0.0542

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.193 AC: 29432 AN: 152246 Hom.: 3641 Cov.: 33 AF XY: 0.193 AC XY: 14391 AN XY: 74424

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.205

Alfa AF: 0.231 Hom.: 622

Bravo AF: 0.180

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.0
Dann	Benign	0.69

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: rs13035033; hg19: chr2-171332288;