rs2132517
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014633.5(CTR9):c.2227-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,594,652 control chromosomes in the GnomAD database, including 29,951 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.27 ( 9379 hom., cov: 33)
Exomes 𝑓: 0.14 ( 20572 hom. )
Consequence
CTR9
NM_014633.5 intron
NM_014633.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.368
Genes affected
CTR9 (HGNC:16850): (CTR9 homolog, Paf1/RNA polymerase II complex component) The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 11-10770436-G-A is Benign according to our data. Variant chr11-10770436-G-A is described in ClinVar as [Benign]. Clinvar id is 1234240.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTR9 | NM_014633.5 | c.2227-51G>A | intron_variant | ENST00000361367.7 | |||
CTR9 | NM_001346279.2 | c.2227-51G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTR9 | ENST00000361367.7 | c.2227-51G>A | intron_variant | 1 | NM_014633.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41671AN: 151990Hom.: 9359 Cov.: 33
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GnomAD3 exomes AF: 0.188 AC: 45161AN: 240396Hom.: 6492 AF XY: 0.175 AC XY: 22774AN XY: 130168
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GnomAD4 exome AF: 0.144 AC: 208394AN: 1442544Hom.: 20572 Cov.: 29 AF XY: 0.143 AC XY: 102451AN XY: 716904
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GnomAD4 genome ? AF: 0.274 AC: 41742AN: 152108Hom.: 9379 Cov.: 33 AF XY: 0.271 AC XY: 20145AN XY: 74374
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at