dbSNP rs115083063: MYO1C:c.2968-52G>T (chr17-1467629-C-A) – 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.2968-52G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00853 in 1,545,948 control chromosomes in the GnomAD database, including 930 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.039 ( 384 hom., cov: 27)

Exomes 𝑓: 0.0055 ( 546 hom. )

Consequence

MYO1C
NM_001080779.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.206

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=-0.82).

BP6

Variant 17-1467629-C-A is Benign according to our data. Variant chr17-1467629-C-A is described in ClinVar as [Benign]. Clinvar id is 1273128.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO1C	NM_001080779.2 link	c.2968-52G>T		intron_variant	Intron 29 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.2968-52G>T		intron_variant	Intron 29 of 31		NM_001080779.2	ENSP00000496954.1		O00159-1

Frequencies

GnomAD3 genomes

AF:

0.0387

AC:

5438

AN:

140394

Hom.:

385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0168

Gnomad ASJ

AF:

0.00414

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000460

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000721

Gnomad OTH

AF:

0.0372

GnomAD3 exomes

AF:

0.0132

AC:

3118

AN:

235608

Hom.:

197

AF XY:

0.00989

AC XY:

1272

AN XY:

128600

show subpopulations

Gnomad AFR exome

AF:

0.171

Gnomad AMR exome

AF:

0.00901

Gnomad ASJ exome

AF:

0.00411

Gnomad EAS exome

AF:

0.0000559

Gnomad SAS exome

AF:

0.000566

Gnomad FIN exome

AF:

0.0000635

Gnomad NFE exome

AF:

0.000690

Gnomad OTH exome

AF:

0.00783

GnomAD4 exome

AF:

0.00552

AC:

7759

AN:

1405452

Hom.:

546

Cov.:

AF XY:

0.00486

AC XY:

3407

AN XY:

701438

show subpopulations

Gnomad4 AFR exome

AF:

0.176

Gnomad4 AMR exome

AF:

0.0108

Gnomad4 ASJ exome

AF:

0.00392

Gnomad4 EAS exome

AF:

0.0000509

Gnomad4 SAS exome

AF:

0.000661

Gnomad4 FIN exome

AF:

0.0000452

Gnomad4 NFE exome

AF:

0.000558

Gnomad4 OTH exome

AF:

0.0129

GnomAD4 genome

AF:

0.0387

AC:

5433

AN:

140496

Hom.:

384

Cov.:

AF XY:

0.0365

AC XY:

2497

AN XY:

68322

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.0168

Gnomad4 ASJ

AF:

0.00414

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000230

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000721

Gnomad4 OTH

AF:

0.0368

Alfa

AF:

0.00828

Hom.:

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

- -

Jul 01, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.6

DANN

Benign

0.54

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