2-170577315-C-T

Variant names:

• chr2-170577315-C-T
• rs2883782
• NM_138995.5:c.3733+33327C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138995.5. 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
	MYO3B	NM_138995.5	MANE Select	c.3733+33327C>T		intron	N/A	NP_620482.3
	MYO3B	NM_001083615.4		c.3652+33327C>T		intron	N/A	NP_001077084.2
	MYO3B	NR_045682.2		n.3996+33327C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO3B	ENST00000408978.9	TSL:1 MANE Select	c.3733+33327C>T		intron	N/A	ENSP00000386213.4
	MYO3B	ENST00000409044.7	TSL:1	c.3652+33327C>T		intron	N/A	ENSP00000386497.3
	MYO3B	ENST00000317935.10	TSL:2	n.3652+33327C>T		intron	N/A	ENSP00000314650.6

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

African (AFR) AF: 0.349 AC: 14441 AN: 41436

American (AMR) AF: 0.489 AC: 7476 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3472

East Asian (EAS) AF: 0.627 AC: 3247 AN: 5178

South Asian (SAS) AF: 0.432 AC: 2084 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5415 AN: 10560

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31353 AN: 67964

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.451 Hom.: 53230

Bravo AF: 0.438

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.4
DANN	Benign	0.84
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2883782; hg19: chr2-171433825;