Genetic Variant MYO1C:c.3065+35G>A (chr17-1467445-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080779.2(MYO1C):c.3065+35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 1,608,666 control chromosomes in the GnomAD database, including 1,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 465 hom., cov: 30)

Exomes 𝑓: 0.037 ( 1339 hom. )

Consequence

MYO1C
NM_001080779.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0960

Variant links:

Genes affected

MYO1C (HGNC:7597): (myosin IC) This gene encodes a member of the unconventional myosin protein family, which are actin-based molecular motors. The protein is found in the cytoplasm, and one isoform with a unique N-terminus is also found in the nucleus. The nuclear isoform associates with RNA polymerase I and II and functions in transcription initiation. The mouse ortholog of this protein also functions in intracellular vesicle transport to the plasma membrane. Multiple transcript variants encoding different isoforms have been found for this gene. The related gene myosin IE has been referred to as myosin IC in the literature, but it is a distinct locus on chromosome 19. [provided by RefSeq, Jul 2008]

MYO1C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 17-1467445-C-T is Benign according to our data. Variant chr17-1467445-C-T is described in ClinVar as [Benign]. Clinvar id is 682721.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1C	NM_001080779.2 link	c.3065+35G>A		intron_variant	Intron 30 of 31	ENST00000648651.1	NP_001074248.1	O00159-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO1C	ENST00000648651.1 link	c.3065+35G>A		intron_variant	Intron 30 of 31		NM_001080779.2	ENSP00000496954.1		O00159-1

Frequencies

GnomAD3 genomes

AF:

0.0634

AC:

9622

AN:

151862

Hom.:

463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.0298

Gnomad AMR

AF:

0.0322

Gnomad ASJ

AF:

0.0927

Gnomad EAS

AF:

0.000775

Gnomad SAS

AF:

0.0346

Gnomad FIN

AF:

0.0220

Gnomad MID

AF:

0.0481

Gnomad NFE

AF:

0.0379

Gnomad OTH

AF:

0.0403

GnomAD3 exomes

AF:

0.0395

AC:

9638

AN:

244164

Hom.:

290

AF XY:

0.0384

AC XY:

5109

AN XY:

133034

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.0217

Gnomad ASJ exome

AF:

0.0867

Gnomad EAS exome

AF:

0.0000549

Gnomad SAS exome

AF:

0.0381

Gnomad FIN exome

AF:

0.0187

Gnomad NFE exome

AF:

0.0365

Gnomad OTH exome

AF:

0.0400

GnomAD4 exome

AF:

0.0375

AC:

54556

AN:

1456686

Hom.:

1339

Cov.:

AF XY:

0.0378

AC XY:

27389

AN XY:

724882

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.0229

Gnomad4 ASJ exome

AF:

0.0855

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0397

Gnomad4 FIN exome

AF:

0.0207

Gnomad4 NFE exome

AF:

0.0353

Gnomad4 OTH exome

AF:

0.0424

GnomAD4 genome

AF:

0.0634

AC:

9641

AN:

151980

Hom.:

465

Cov.:

AF XY:

0.0609

AC XY:

4524

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.0322

Gnomad4 ASJ

AF:

0.0927

Gnomad4 EAS

AF:

0.000776

Gnomad4 SAS

AF:

0.0346

Gnomad4 FIN

AF:

0.0220

Gnomad4 NFE

AF:

0.0380

Gnomad4 OTH

AF:

0.0399

Alfa

AF:

0.0572

Hom.:

Bravo

AF:

0.0667

Asia WGS

AF:

0.0220

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 16, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.7

DANN

Benign

0.86

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