chr10-17218291-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_108061.1(VIM-AS1):n.642-2017T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,006 control chromosomes in the GnomAD database, including 13,922 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 0.42 ( 13922 hom., cov: 32)
Consequence
VIM-AS1
NR_108061.1 intron, non_coding_transcript
NR_108061.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.557
Genes affected
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VIM-AS1 | NR_108061.1 | n.642-2017T>C | intron_variant, non_coding_transcript_variant | ||||
VIM-AS1 | NR_108060.1 | n.44-616T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIM-AS1 | ENST00000605833.2 | n.675-2017T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
VIM-AS1 | ENST00000437232.5 | n.44-616T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
VIM-AS1 | ENST00000661048.1 | n.77-2927T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63988AN: 151888Hom.: 13921 Cov.: 32
GnomAD3 genomes
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AF:
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63988
AN:
151888
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Cov.:
32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.421 AC: 64019AN: 152006Hom.: 13922 Cov.: 32 AF XY: 0.426 AC XY: 31659AN XY: 74292
GnomAD4 genome
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AC:
64019
AN:
152006
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32
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31659
AN XY:
74292
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2059
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at