rs11871508
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_016078.6(TVP23B):c.462+1775G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 151,890 control chromosomes in the GnomAD database, including 28 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: 𝑓 0.016 ( 28 hom., cov: 30)
Consequence
TVP23B
NM_016078.6 intron
NM_016078.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Genes affected
TVP23B (HGNC:20399): (trans-golgi network vesicle protein 23 homolog B) Predicted to be involved in protein secretion and vesicle-mediated transport. Predicted to be integral component of membrane. Predicted to be integral component of Golgi membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0163 (2473/151890) while in subpopulation NFE AF= 0.0249 (1689/67930). AF 95% confidence interval is 0.0239. There are 28 homozygotes in gnomad4. There are 1155 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 28 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TVP23B | NM_016078.6 | c.462+1775G>A | intron_variant | ENST00000307767.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TVP23B | ENST00000307767.13 | c.462+1775G>A | intron_variant | 1 | NM_016078.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2477AN: 151772Hom.: 28 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0163 AC: 2473AN: 151890Hom.: 28 Cov.: 30 AF XY: 0.0156 AC XY: 1155AN XY: 74244
GnomAD4 genome
?
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30
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1155
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74244
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16
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3470
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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