NM_018728.4:c.4296+670C>T

Variant names:

• chr15-52211060-G-A
• rs1011051
• NM_018728.4:c.4296+670C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018728.4(MYO5C):​c.4296+670C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,010 control chromosomes in the GnomAD database, including 23,474 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (23474 hom., cov: 31)
• Consequence: MYO5C NM_018728.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 11 publications found

Genes affected

MYO5C (HGNC:7604): (myosin VC) Predicted to enable actin filament binding activity and microfilament motor activity. Predicted to be involved in actin filament organization and vesicle transport along actin filament. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CERNA1 (HGNC:52664): (competing endogenous lncRNA 1 for miR-4707-5p and miR-4767)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018728.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO5C	NM_018728.4	MANE Select	c.4296+670C>T		intron	N/A	NP_061198.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYO5C	ENST00000261839.12	TSL:1 MANE Select	c.4296+670C>T		intron	N/A	ENSP00000261839.7
	MYO5C	ENST00000559696.1	TSL:5	n.496+670C>T		intron	N/A
	MYO5C	ENST00000560809.5	TSL:2	n.*3070+670C>T		intron	N/A	ENSP00000453641.1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77648 AN: 151892 Hom.: 23478 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.511 AC: 77655 AN: 152010 Hom.: 23474 Cov.: 31 AF XY: 0.507 AC XY: 37639 AN XY: 74290

African (AFR) AF: 0.210 AC: 8713 AN: 41460

American (AMR) AF: 0.483 AC: 7378 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2432 AN: 3464

East Asian (EAS) AF: 0.229 AC: 1184 AN: 5168

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4818

European-Finnish (FIN) AF: 0.677 AC: 7155 AN: 10568

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47083 AN: 67950

Other (OTH) AF: 0.533 AC: 1124 AN: 2108

Alfa AF: 0.612 Hom.: 14522

Bravo AF: 0.480

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.098
DANN	Benign	0.37
PhyloP100		-2.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1011051; hg19: chr15-52503257;