rs2928378
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_016208.4(VPS28):āc.432T>Cā(p.Arg144=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.996 in 1,606,404 control chromosomes in the GnomAD database, including 797,545 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: š 0.98 ( 73194 hom., cov: 35)
Exomes š: 1.0 ( 724351 hom. )
Consequence
VPS28
NM_016208.4 synonymous
NM_016208.4 synonymous
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0450
Genes affected
VPS28 (HGNC:18178): (VPS28 subunit of ESCRT-I) This gene encodes a protein subunit of the ESCRT-I complex (endosomal complexes required for transport), which functions in the transport and sorting of proteins into subcellular vesicles. This complex can also be hijacked to facilitate the budding of enveloped viruses from the cell membrane. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
?
Synonymous conserved (PhyloP=0.045 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS28 | NM_016208.4 | c.432T>C | p.Arg144= | synonymous_variant | 8/10 | ENST00000292510.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS28 | ENST00000292510.6 | c.432T>C | p.Arg144= | synonymous_variant | 8/10 | 1 | NM_016208.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.980 AC: 149140AN: 152204Hom.: 73146 Cov.: 35
GnomAD3 genomes
?
AF:
AC:
149140
AN:
152204
Hom.:
Cov.:
35
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.998 AC: 1451296AN: 1454082Hom.: 724351 Cov.: 89 AF XY: 0.998 AC XY: 721305AN XY: 722488
GnomAD4 exome
AF:
AC:
1451296
AN:
1454082
Hom.:
Cov.:
89
AF XY:
AC XY:
721305
AN XY:
722488
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.980 AC: 149245AN: 152322Hom.: 73194 Cov.: 35 AF XY: 0.980 AC XY: 73001AN XY: 74478
GnomAD4 genome
?
AF:
AC:
149245
AN:
152322
Hom.:
Cov.:
35
AF XY:
AC XY:
73001
AN XY:
74478
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at