17-1467804-A-G

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.2967+36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.053 (607 hom., cov: 13)
  • Exomes 𝑓: 0.0056 (408 hom.)
• Consequence: MYO1C NM_001080779.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.97

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=-0.86).
• BP6: Variant 17-1467804-A-G is Benign according to our data. Variant chr17-1467804-A-G is described in ClinVar as [Benign]. Clinvar id is 1247147.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO1C	NM_001080779.2	c.2967+36T>C		intron_variant		ENST00000648651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO1C	ENST00000648651.1	c.2967+36T>C		intron_variant			NM_001080779.2

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 5112 AN: 95878 Hom.: 608 Cov.: 13

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.00585

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00110

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000908

Gnomad OTH AF: 0.0485

GnomAD3 exomes AF: 0.0248 AC: 1968 AN: 79222 Hom.: 175 AF XY: 0.0189 AC XY: 848 AN XY: 44944

Gnomad AFR exome AF: 0.299

Gnomad AMR exome AF: 0.0518

Gnomad ASJ exome AF: 0.00730

Gnomad EAS exome AF: 0.000284

Gnomad SAS exome AF: 0.00113

Gnomad FIN exome AF: 0.0000951

Gnomad NFE exome AF: 0.00109

Gnomad OTH exome AF: 0.0217

GnomAD4 exome AF: 0.00558 AC: 4297 AN: 770570 Hom.: 408 Cov.: 11 AF XY: 0.00466 AC XY: 1872 AN XY: 401350

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.0111

Gnomad4 ASJ exome AF: 0.00326

Gnomad4 EAS exome AF: 0.0000328

Gnomad4 SAS exome AF: 0.000633

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000516

Gnomad4 OTH exome AF: 0.0133

GnomAD4 genome AF: 0.0532 AC: 5109 AN: 95958 Hom.: 607 Cov.: 13 AF XY: 0.0529 AC XY: 2365 AN XY: 44746

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0247

Gnomad4 ASJ AF: 0.00585

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000551

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000908

Gnomad4 OTH AF: 0.0481

Alfa AF: 0.00841 Hom.: 21

Bravo AF: 0.0675

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 13, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.20

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: rs141538791; hg19: chr17-1371098;