17-1465529-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_001080779.2(MYO1C):c.*197C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 497,876 control chromosomes in the GnomAD database, including 1,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.053 (298 hom., cov: 32)
  • Exomes 𝑓: 0.062 (770 hom.)
• Consequence: MYO1C NM_001080779.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.48

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BP6: Variant 17-1465529-G-A is Benign according to our data. Variant chr17-1465529-G-A is described in ClinVar as [Benign]. Clinvar id is 1183863.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1C	NM_001080779.2	c.*197C>T		3_prime_UTR_variant	32/32	ENST00000648651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1C	ENST00000648651.1	c.*197C>T		3_prime_UTR_variant	32/32		NM_001080779.2

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8123 AN: 152132 Hom.: 299 Cov.: 32

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0618

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0565

GnomAD4 exome AF: 0.0623 AC: 21532 AN: 345626 Hom.: 770 Cov.: 5 AF XY: 0.0634 AC XY: 11060 AN XY: 174546

Gnomad4 AFR exome AF: 0.0192

Gnomad4 AMR exome AF: 0.0390

Gnomad4 ASJ exome AF: 0.129

Gnomad4 EAS exome AF: 0.000788

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.0640

Gnomad4 NFE exome AF: 0.0660

Gnomad4 OTH exome AF: 0.0679

GnomAD4 genome AF: 0.0533 AC: 8120 AN: 152250 Hom.: 298 Cov.: 32 AF XY: 0.0546 AC XY: 4065 AN XY: 74446

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0618

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0597 Hom.: 60

Bravo AF: 0.0492

Asia WGS AF: 0.0590 AC: 205 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

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	14
Dann	Benign	0.83

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: rs11538162; hg19: chr17-1368823;