rs755625059
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_007126.5(VCP):c.2316-4A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,614,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007126.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VCP | NM_007126.5 | c.2316-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000358901.11 | |||
VCP | NM_001354927.2 | c.2181-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
VCP | NM_001354928.2 | c.2181-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VCP | ENST00000358901.11 | c.2316-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_007126.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251386Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135872
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.0000619 AC XY: 45AN XY: 727208
GnomAD4 genome ? AF: 0.0000853 AC: 13AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
Inclusion body myopathy with Paget disease of bone and frontotemporal dementia;C5436279:Frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at