rs12903401
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000560872.1(ANKRD34C-AS1):n.178-17652C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 501,760 control chromosomes in the GnomAD database, including 52,598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.41 ( 13946 hom., cov: 32)
Exomes 𝑓: 0.46 ( 38652 hom. )
Consequence
ANKRD34C-AS1
ENST00000560872.1 intron
ENST00000560872.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.402
Genes affected
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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=-0.68).
BP6
Variant 15-79209754-G-C is Benign according to our data. Variant chr15-79209754-G-C is described in ClinVar as [Benign]. Clinvar id is 1223338.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD34C-AS1 | NR_038997.1 | n.298-17652C>G | intron_variant | |||||
MIR184 | NR_029705.1 | n.-34G>C | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD34C-AS1 | ENST00000559225.2 | n.436+3433C>G | intron_variant | 4 | ||||||
ANKRD34C-AS1 | ENST00000560872.1 | n.178-17652C>G | intron_variant | 3 | ||||||
ANKRD34C-AS1 | ENST00000661423.1 | n.339-17652C>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.406 AC: 61592AN: 151888Hom.: 13937 Cov.: 32
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GnomAD3 exomes AF: 0.464 AC: 115006AN: 247820Hom.: 27733 AF XY: 0.462 AC XY: 61934AN XY: 134128
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GnomAD4 exome AF: 0.461 AC: 161409AN: 349756Hom.: 38652 Cov.: 0 AF XY: 0.453 AC XY: 89226AN XY: 197054
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GnomAD4 genome AF: 0.405 AC: 61610AN: 152004Hom.: 13946 Cov.: 32 AF XY: 0.409 AC XY: 30358AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at