rs34835605
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000557658.6(VIPAS39):c.1179+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 1,612,142 control chromosomes in the GnomAD database, including 29,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2248 hom., cov: 32)
Exomes 𝑓: 0.19 ( 27275 hom. )
Consequence
VIPAS39
ENST00000557658.6 intron
ENST00000557658.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.10
Genes affected
VIPAS39 (HGNC:20347): (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog) Involved in endosome to lysosome transport and intracellular protein transport. Acts upstream of or within collagen metabolic process and peptidyl-lysine hydroxylation. Located in Golgi apparatus and endosome. Implicated in arthrogryposis, renal dysfunction, and cholestasis 2. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 14-77433822-C-T is Benign according to our data. Variant chr14-77433822-C-T is described in ClinVar as [Benign]. Clinvar id is 261486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VIPAS39 | NM_001193315.2 | c.1179+20G>A | intron_variant | ENST00000557658.6 | NP_001180244.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VIPAS39 | ENST00000557658.6 | c.1179+20G>A | intron_variant | 1 | NM_001193315.2 | ENSP00000452191 | P1 |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23844AN: 151986Hom.: 2246 Cov.: 32
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GnomAD3 exomes AF: 0.186 AC: 46564AN: 250862Hom.: 4987 AF XY: 0.189 AC XY: 25624AN XY: 135568
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GnomAD4 exome AF: 0.188 AC: 273988AN: 1460038Hom.: 27275 Cov.: 31 AF XY: 0.190 AC XY: 137754AN XY: 726440
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GnomAD4 genome AF: 0.157 AC: 23858AN: 152104Hom.: 2248 Cov.: 32 AF XY: 0.157 AC XY: 11680AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 02, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at