2-170577315-C-T

Position:

• chr2-170577315-C-T

Variant summary

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

The NM_138995.5(MYO3B):​c.3733+33327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,038 control chromosomes in the GnomAD database, including 15,183 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 0.44 (15183 hom., cov: 33)
• Consequence: MYO3B NM_138995.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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]

MYO3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO3B	NM_138995.5	c.3733+33327C>T		intron_variant		ENST00000408978.9	NP_620482.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO3B	ENST00000408978.9	c.3733+33327C>T		intron_variant		1	NM_138995.5	ENSP00000386213.4

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66961 AN: 151920 Hom.: 15176 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.441 AC: 66999 AN: 152038 Hom.: 15183 Cov.: 33 AF XY: 0.444 AC XY: 32975 AN XY: 74334

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.407

Alfa AF: 0.454 Hom.: 33960

Bravo AF: 0.438

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.4
DANN	Benign	0.84

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: rs2883782; hg19: chr2-171433825;