17-1467426-C-T

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.3065+54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,598,196 control chromosomes in the GnomAD database, including 130,154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (9898 hom., cov: 28)
  • Exomes 𝑓: 0.41 (120256 hom.)
• Consequence: MYO1C NM_001080779.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.551

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=-0.85).
• BP6: Variant 17-1467426-C-T is Benign according to our data. Variant chr17-1467426-C-T is described in ClinVar as [Benign]. Clinvar id is 1254983.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1C	NM_001080779.2	c.3065+54G>A		intron_variant		ENST00000648651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1C	ENST00000648651.1	c.3065+54G>A		intron_variant			NM_001080779.2

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53526 AN: 151020 Hom.: 9899 Cov.: 28

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.405 AC: 586096 AN: 1447060 Hom.: 120256 Cov.: 33 AF XY: 0.406 AC XY: 292455 AN XY: 720094

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.364

Gnomad4 ASJ exome AF: 0.348

Gnomad4 EAS exome AF: 0.356

Gnomad4 SAS exome AF: 0.422

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.383

GnomAD4 genome AF: 0.354 AC: 53558 AN: 151136 Hom.: 9898 Cov.: 28 AF XY: 0.352 AC XY: 25936 AN XY: 73784

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.383

Alfa AF: 0.377 Hom.: 1373

Bravo AF: 0.353

Asia WGS AF: 0.369 AC: 1282 AN: 3476

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 22, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.6
Dann	Benign	0.75

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: rs2302457; hg19: chr17-1370720; COSMIC: COSV63000074; COSMIC: COSV63000074;