rs1011051

Positions:

• chr15-52211060-G-A
• chr15-52211060-G-C
• chr15-52211060-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYO5C	NM_018728.4	c.4296+670C>T		intron_variant		ENST00000261839.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYO5C	ENST00000261839.12	c.4296+670C>T		intron_variant		1	NM_018728.4	P1
MYO5C	ENST00000560809.5	c.*3070+670C>T		intron_variant, NMD_transcript_variant		2
MYO5C	ENST00000559696.1	n.496+670C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.533

Alfa AF: 0.604 Hom.: 12717

Bravo AF: 0.480

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.098
DANN	Benign	0.37

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: rs1011051; hg19: chr15-52503257;