15-52242147-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_018728.4(MYO5C):​c.2457C>A​(p.Arg819Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

MYO5C
NM_018728.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
Synonymous conserved (PhyloP=-1.24 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MYO5CNM_018728.4 linkc.2457C>A p.Arg819Arg synonymous_variant Exon 20 of 41 ENST00000261839.12 NP_061198.2 Q9NQX4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MYO5CENST00000261839.12 linkc.2457C>A p.Arg819Arg synonymous_variant Exon 20 of 41 1 NM_018728.4 ENSP00000261839.7 Q9NQX4-1
MYO5CENST00000559434.1 linkn.1413C>A non_coding_transcript_exon_variant Exon 1 of 3 2
MYO5CENST00000558902.5 linkn.*2072+2209C>A intron_variant Intron 20 of 23 2 ENSP00000453517.1 H0YM96
MYO5CENST00000560809.5 linkn.*1493+2209C>A intron_variant Intron 19 of 37 2 ENSP00000453641.1 H0YMK3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
49
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.050
DANN
Benign
0.39
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-52534344; API