17-1466044-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001080779.2(MYO1C):c.3166-292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,024 control chromosomes in the GnomAD database, including 717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.096 (717 hom., cov: 31)
• Consequence: MYO1C NM_001080779.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.893

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 17-1466044-T-C is Benign according to our data. Variant chr17-1466044-T-C is described in ClinVar as [Benign]. Clinvar id is 1249204.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1C	NM_001080779.2	c.3166-292A>G		intron_variant		ENST00000648651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1C	ENST00000648651.1	c.3166-292A>G		intron_variant			NM_001080779.2

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14524 AN: 151906 Hom.: 712 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0957 AC: 14553 AN: 152024 Hom.: 717 Cov.: 31 AF XY: 0.0923 AC XY: 6856 AN XY: 74314

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0784

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.0702

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0657 Hom.: 74

Bravo AF: 0.0979

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	5.1
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs112614619; hg19: chr17-1369338;