NM_013291.3:c.937+24G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013291.3(CPSF1):c.937+24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 127,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000016 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CPSF1
NM_013291.3 intron
NM_013291.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.95
Publications
3 publications found
Genes affected
CPSF1 (HGNC:2324): (cleavage and polyadenylation specific factor 1) Cleavage and polyadenylation specificity factor (CPSF) is a multisubunit complex that plays a central role in 3-prime processing of pre-mRNAs. CPSF recognizes the AAUAAA signal in the pre-mRNA and interacts with other proteins to facilitate both RNA cleavage and poly(A) synthesis. CPSF1 is the largest subunit of the CPSF complex (Murthy and Manley, 1995 [PubMed 7590244]).[supplied by OMIM, Mar 2008]
MIR1234 (HGNC:33926): (microRNA 1234) 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]
MIR6849 (HGNC:49991): (microRNA 6849) 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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (Cadd=0.245).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_013291.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes 0.0000157 AC: 2AN: 127252Hom.: 0 Cov.: 26 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
127252
Hom.:
Cov.:
26
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 Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1120950Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 557452
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1120950
Hom.:
Cov.:
19
AF XY:
AC XY:
0
AN XY:
557452
African (AFR)
AF:
AC:
0
AN:
27280
American (AMR)
AF:
AC:
0
AN:
32564
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20452
East Asian (EAS)
AF:
AC:
0
AN:
34896
South Asian (SAS)
AF:
AC:
0
AN:
69208
European-Finnish (FIN)
AF:
AC:
0
AN:
39310
Middle Eastern (MID)
AF:
AC:
0
AN:
3362
European-Non Finnish (NFE)
AF:
AC:
0
AN:
845332
Other (OTH)
AF:
AC:
0
AN:
48546
GnomAD4 genome 0.0000157 AC: 2AN: 127340Hom.: 0 Cov.: 26 AF XY: 0.0000321 AC XY: 2AN XY: 62244 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
127340
Hom.:
Cov.:
26
AF XY:
AC XY:
2
AN XY:
62244
show subpopulations
African (AFR)
AF:
AC:
1
AN:
36280
American (AMR)
AF:
AC:
0
AN:
13688
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2854
East Asian (EAS)
AF:
AC:
0
AN:
4472
South Asian (SAS)
AF:
AC:
0
AN:
3754
European-Finnish (FIN)
AF:
AC:
0
AN:
9892
Middle Eastern (MID)
AF:
AC:
0
AN:
260
European-Non Finnish (NFE)
AF:
AC:
1
AN:
53746
Other (OTH)
AF:
AC:
0
AN:
1706
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
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
Genome Het
Variant carriers
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10
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30-35
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Age
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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