Variant 17-1467248-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001080779.2(MYO1C):c.3159G>T(p.Leu1053=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0968 in 1,611,446 control chromosomes in the GnomAD database, including 8,060 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.097 ( 747 hom., cov: 32)

Exomes 𝑓: 0.097 ( 7313 hom. )

Consequence

MYO1C
NM_001080779.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.653

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BP6

Variant 17-1467248-C-A is Benign according to our data. Variant chr17-1467248-C-A is described in ClinVar as [Benign]. Clinvar id is 508122.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.653 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYO1C	NM_001080779.2 linkuse as main transcript	c.3159G>T	p.Leu1053=	synonymous_variant	31/32	ENST00000648651.1	NP_001074248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYO1C	ENST00000648651.1 linkuse as main transcript	c.3159G>T	p.Leu1053=	synonymous_variant	31/32		NM_001080779.2	ENSP00000496954		O00159-1

Frequencies

GnomAD3 genomes

AF:

0.0973

AC:

14811

AN:

152142

Hom.:

742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.0792

Gnomad ASJ

AF:

0.0605

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.0700

Gnomad FIN

AF:

0.0418

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0967

GnomAD3 exomes

AF:

0.0808

AC:

19771

AN:

244766

Hom.:

837

AF XY:

0.0809

AC XY:

10746

AN XY:

132758

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.0520

Gnomad ASJ exome

AF:

0.0571

Gnomad EAS exome

AF:

0.0874

Gnomad SAS exome

AF:

0.0643

Gnomad FIN exome

AF:

0.0469

Gnomad NFE exome

AF:

0.0966

Gnomad OTH exome

AF:

0.0858

GnomAD4 exome

AF:

0.0967

AC:

141157

AN:

1459186

Hom.:

7313

Cov.:

AF XY:

0.0956

AC XY:

69371

AN XY:

725670

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.0546

Gnomad4 ASJ exome

AF:

0.0604

Gnomad4 EAS exome

AF:

0.132

Gnomad4 SAS exome

AF:

0.0647

Gnomad4 FIN exome

AF:

0.0494

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.0895

GnomAD4 genome

AF:

0.0975

AC:

14839

AN:

152260

Hom.:

747

Cov.:

AF XY:

0.0939

AC XY:

6994

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.0789

Gnomad4 ASJ

AF:

0.0605

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.0694

Gnomad4 FIN

AF:

0.0418

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0961

Alfa

AF:

0.0974

Hom.:

877

Bravo

AF:

0.0998

Asia WGS

AF:

0.0940

AC:

326

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 09, 2017

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. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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