rs112062894
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001193315.2(VIPAS39):c.598-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00025 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001193315.2 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 |
---|---|---|---|---|---|---|---|
VIPAS39 | NM_001193315.2 | c.598-25C>T | intron_variant | ENST00000557658.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIPAS39 | ENST00000557658.6 | c.598-25C>T | intron_variant | 1 | NM_001193315.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00115 AC: 175AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000279 AC: 70AN: 250606Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135514
GnomAD4 exome AF: 0.000152 AC: 222AN: 1461798Hom.: 0 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 727206
GnomAD4 genome ? AF: 0.00119 AC: 181AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.00133 AC XY: 99AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at