NM_001325.3:c.1140C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001325.3(CSTF2):c.1140C>T(p.Pro380Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00428 in 1,207,897 control chromosomes in the GnomAD database, including 146 homozygotes. There are 1,383 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 69 hom., 673 hem., cov: 22)
Exomes 𝑓: 0.0025 ( 77 hom. 710 hem. )
Consequence
CSTF2
NM_001325.3 synonymous
NM_001325.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0420
Genes affected
CSTF2 (HGNC:2484): (cleavage stimulation factor subunit 2) This gene encodes a nuclear protein with an RRM (RNA recognition motif) domain. The protein is a member of the cleavage stimulation factor (CSTF) complex that is involved in the 3' end cleavage and polyadenylation of pre-mRNAs. Specifically, this protein binds GU-rich elements within the 3'-untranslated region of mRNAs. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant X-100832842-C-T is Benign according to our data. Variant chrX-100832842-C-T is described in ClinVar as [Benign]. Clinvar id is 781552.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.042 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0731 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSTF2 | NM_001325.3 | c.1140C>T | p.Pro380Pro | synonymous_variant | Exon 10 of 14 | ENST00000372972.7 | NP_001316.1 | |
CSTF2 | NM_001306206.2 | c.1200C>T | p.Pro400Pro | synonymous_variant | Exon 11 of 15 | NP_001293135.1 | ||
CSTF2 | NM_001306209.2 | c.1089C>T | p.Pro363Pro | synonymous_variant | Exon 10 of 14 | NP_001293138.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSTF2 | ENST00000372972.7 | c.1140C>T | p.Pro380Pro | synonymous_variant | Exon 10 of 14 | 1 | NM_001325.3 | ENSP00000362063.2 | ||
CSTF2 | ENST00000415585.7 | c.1200C>T | p.Pro400Pro | synonymous_variant | Exon 11 of 15 | 1 | ENSP00000387996.2 | |||
CSTF2 | ENST00000475126.5 | n.1089C>T | non_coding_transcript_exon_variant | Exon 10 of 14 | 5 | ENSP00000432060.1 |
Frequencies
GnomAD3 genomes AF: 0.0219 AC: 2449AN: 111873Hom.: 66 Cov.: 22 AF XY: 0.0195 AC XY: 664AN XY: 34085
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GnomAD3 exomes AF: 0.00635 AC: 1119AN: 176296Hom.: 35 AF XY: 0.00388 AC XY: 238AN XY: 61282
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GnomAD4 exome AF: 0.00247 AC: 2706AN: 1095972Hom.: 77 Cov.: 31 AF XY: 0.00196 AC XY: 710AN XY: 361464
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GnomAD4 genome AF: 0.0220 AC: 2466AN: 111925Hom.: 69 Cov.: 22 AF XY: 0.0197 AC XY: 673AN XY: 34147
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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
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at