rs794728003
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The ENST00000421939.5(CDK9):c.153C>G(p.Leu51Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000076 in 263,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000088 ( 0 hom. )
Consequence
CDK9
ENST00000421939.5 synonymous
ENST00000421939.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.160
Publications
0 publications found
Genes affected
CDK9 (HGNC:1780): (cyclin dependent kinase 9) The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and known as important cell cycle regulators. This kinase was found to be a component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II-directed transcription and functions by phosphorylating the C-terminal domain of the largest subunit of RNA polymerase II. This protein forms a complex with and is regulated by its regulatory subunit cyclin T or cyclin K. HIV-1 Tat protein was found to interact with this protein and cyclin T, which suggested a possible involvement of this protein in AIDS. [provided by RefSeq, Jul 2008]
MIR2861 (HGNC:38221): (microRNA 2861) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of target mRNAs. This microRNA may play a role in osteoblast differentiation and a mutation in this gene is associated with osteoporosis. Altered expression of this microRNA has been observed in human cancers, with reduced expression seen in cervical cancer, while expression in papillary thyroid carcinoma (PTC) is increased. [provided by RefSeq, Mar 2017]
MIR3960 (HGNC:41595): (microRNA 3960) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP7
Synonymous conserved (PhyloP=0.16 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000421939.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MIR2861 | NR_036055.1 | n.33C>G | non_coding_transcript_exon | Exon 1 of 1 | |||||
| CDK9 | NM_001261.4 | MANE Select | c.-199C>G | upstream_gene | N/A | NP_001252.1 | |||
| MIR3960 | NR_039767.1 | n.*27C>G | downstream_gene | N/A |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CDK9 | ENST00000421939.5 | TSL:3 | c.153C>G | p.Leu51Leu | synonymous | Exon 1 of 3 | ENSP00000395872.1 | ||
| MIR2861 | ENST00000636310.1 | TSL:6 | n.33C>G | non_coding_transcript_exon | Exon 1 of 1 | ||||
| CDK9 | ENST00000373264.5 | TSL:1 MANE Select | c.-199C>G | upstream_gene | N/A | ENSP00000362361.4 |
Frequencies
GnomAD3 genomes 0.00000669 AC: 1AN: 149550Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
149550
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000880 AC: 1AN: 113690Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0AN XY: 61392 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
113690
Hom.:
Cov.:
2
AF XY:
AC XY:
0
AN XY:
61392
show subpopulations
African (AFR)
AF:
AC:
0
AN:
2638
American (AMR)
AF:
AC:
0
AN:
2810
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3512
East Asian (EAS)
AF:
AC:
0
AN:
8584
South Asian (SAS)
AF:
AC:
0
AN:
2310
European-Finnish (FIN)
AF:
AC:
0
AN:
10444
Middle Eastern (MID)
AF:
AC:
0
AN:
562
European-Non Finnish (NFE)
AF:
AC:
1
AN:
75980
Other (OTH)
AF:
AC:
0
AN:
6850
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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60-65
65-70
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>80
Age
GnomAD4 genome 0.00000669 AC: 1AN: 149550Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 1AN XY: 72988 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
149550
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
72988
show subpopulations
African (AFR)
AF:
AC:
0
AN:
40998
American (AMR)
AF:
AC:
0
AN:
15082
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3438
East Asian (EAS)
AF:
AC:
0
AN:
5056
South Asian (SAS)
AF:
AC:
0
AN:
4810
European-Finnish (FIN)
AF:
AC:
0
AN:
9906
Middle Eastern (MID)
AF:
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67006
Other (OTH)
AF:
AC:
0
AN:
2050
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:association
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
-
BONE MINERAL DENSITY QUANTITATIVE TRAIT LOCUS 15 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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