Variant 2-170217377-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_138995.5(MYO3B):c.585G>A(p.Pro195=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,612,708 control chromosomes in the GnomAD database, including 250,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 24080 hom., cov: 33)

Exomes 𝑓: 0.55 ( 226111 hom. )

Consequence

MYO3B
NM_138995.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.82

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 2-170217377-G-A is Benign according to our data. Variant chr2-170217377-G-A is described in ClinVar as [Benign]. Clinvar id is 1246117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.82 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO3B	NM_138995.5 linkuse as main transcript	c.585G>A	p.Pro195=	synonymous_variant	6/35	ENST00000408978.9	NP_620482.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO3B	ENST00000408978.9 linkuse as main transcript	c.585G>A	p.Pro195=	synonymous_variant	6/35	1	NM_138995.5	ENSP00000386213	P1	Q8WXR4-1

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

85186

AN:

151988

Hom.:

24077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.702

Gnomad AMR

AF:

0.441

Gnomad ASJ

AF:

0.593

Gnomad EAS

AF:

0.573

Gnomad SAS

AF:

0.625

Gnomad FIN

AF:

0.582

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.542

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.548

AC:

136838

AN:

249546

Hom.:

38271

AF XY:

0.556

AC XY:

75237

AN XY:

135392

show subpopulations

Gnomad AFR exome

AF:

0.620

Gnomad AMR exome

AF:

0.400

Gnomad ASJ exome

AF:

0.586

Gnomad EAS exome

AF:

0.584

Gnomad SAS exome

AF:

0.626

Gnomad FIN exome

AF:

0.592

Gnomad NFE exome

AF:

0.546

Gnomad OTH exome

AF:

0.547

GnomAD4 exome

AF:

0.554

AC:

809645

AN:

1460602

Hom.:

226111

Cov.:

AF XY:

0.557

AC XY:

404595

AN XY:

726700

show subpopulations

Gnomad4 AFR exome

AF:

0.620

Gnomad4 AMR exome

AF:

0.405

Gnomad4 ASJ exome

AF:

0.587

Gnomad4 EAS exome

AF:

0.587

Gnomad4 SAS exome

AF:

0.625

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.549

Gnomad4 OTH exome

AF:

0.562

GnomAD4 genome

AF:

0.560

AC:

85233

AN:

152106

Hom.:

24080

Cov.:

AF XY:

0.560

AC XY:

41668

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.617

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.593

Gnomad4 EAS

AF:

0.572

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.582

Gnomad4 NFE

AF:

0.542

Gnomad4 OTH

AF:

0.534

Alfa

AF:

0.547

Hom.:

46157

Bravo

AF:

0.552

Asia WGS

AF:

0.606

AC:

2104

AN:

3478

EpiCase

AF:

0.546

EpiControl

AF:

0.545

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.23

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over