chr15-90999061-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_018668.5(VPS33B):c.1775-7T>C 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 0.0000378 in 1,613,952 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_018668.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS33B | NM_018668.5 | c.1775-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000333371.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS33B | ENST00000333371.8 | c.1775-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018668.5 | P1 | |||
VPS33B | ENST00000535906.1 | c.1694-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
VPS33B | ENST00000574755.5 | c.*1470-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 | |||||
VPS33B | ENST00000557470.5 | n.148-7T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000196 AC: 49AN: 250376Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135396
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461664Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 727094
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at