X-100822260-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001325.3(CSTF2):c.147C>T(p.Tyr49Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,207,129 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000045 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000023 ( 0 hom. 8 hem. )
Consequence
CSTF2
NM_001325.3 synonymous
NM_001325.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.90
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant X-100822260-C-T is Benign according to our data. Variant chrX-100822260-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 745214.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.9 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSTF2 | NM_001325.3 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 14 | ENST00000372972.7 | NP_001316.1 | |
CSTF2 | NM_001306206.2 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 15 | NP_001293135.1 | ||
CSTF2 | NM_001306209.2 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 14 | NP_001293138.1 | ||
CSTF2 | XM_047441854.1 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 10 | XP_047297810.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CSTF2 | ENST00000372972.7 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 14 | 1 | NM_001325.3 | ENSP00000362063.2 | ||
CSTF2 | ENST00000415585.7 | c.147C>T | p.Tyr49Tyr | synonymous_variant | Exon 3 of 15 | 1 | ENSP00000387996.2 | |||
CSTF2 | ENST00000413437.1 | c.120C>T | p.Tyr40Tyr | synonymous_variant | Exon 3 of 6 | 5 | ENSP00000415705.1 | |||
CSTF2 | ENST00000475126.5 | n.147C>T | non_coding_transcript_exon_variant | Exon 3 of 14 | 5 | ENSP00000432060.1 |
Frequencies
GnomAD3 genomes AF: 0.0000449 AC: 5AN: 111441Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33641
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GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181447Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65981
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GnomAD4 exome AF: 0.0000228 AC: 25AN: 1095688Hom.: 0 Cov.: 29 AF XY: 0.0000222 AC XY: 8AN XY: 361138
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GnomAD4 genome AF: 0.0000449 AC: 5AN: 111441Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33641
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 08, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
Calibrated prediction
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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