Genetic Variant MYO3B:c.321+3935C>T (chr2-170204219-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138995.5(MYO3B):c.321+3935C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 152,036 control chromosomes in the GnomAD database, including 22,266 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 0.54 ( 22266 hom., cov: 33)

Consequence

MYO3B
NM_138995.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.893

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO3B	NM_138995.5 link	c.321+3935C>T		intron_variant	Intron 3 of 34	ENST00000408978.9	NP_620482.3	Q8WXR4-1B7ZM71

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO3B	ENST00000408978.9 link	c.321+3935C>T		intron_variant	Intron 3 of 34	1	NM_138995.5	ENSP00000386213.4		Q8WXR4-1

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

82110

AN:

151918

Hom.:

22222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.542

Gnomad SAS

AF:

0.543

Gnomad FIN

AF:

0.522

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.509

Gnomad OTH

AF:

0.548

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

GnomAD4 genome

AF:

0.541

AC:

82211

AN:

152036

Hom.:

22266

Cov.:

AF XY:

0.544

AC XY:

40433

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.571

Gnomad4 AMR

AF:

0.614

Gnomad4 ASJ

AF:

0.535

Gnomad4 EAS

AF:

0.543

Gnomad4 SAS

AF:

0.543

Gnomad4 FIN

AF:

0.522

Gnomad4 NFE

AF:

0.509

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.521

Hom.:

41968

Bravo

AF:

0.549

Asia WGS

AF:

0.570

AC:

1986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.96

DANN

Benign

0.76

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over