X-100832842-C-T

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0420
Variant links:
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
CSTF2NM_001325.3 linkc.1140C>T p.Pro380Pro synonymous_variant Exon 10 of 14 ENST00000372972.7 NP_001316.1 P33240-1
CSTF2NM_001306206.2 linkc.1200C>T p.Pro400Pro synonymous_variant Exon 11 of 15 NP_001293135.1 E7EWR4B3V096B4DUD5
CSTF2NM_001306209.2 linkc.1089C>T p.Pro363Pro synonymous_variant Exon 10 of 14 NP_001293138.1 P33240-2B4DUD5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CSTF2ENST00000372972.7 linkc.1140C>T p.Pro380Pro synonymous_variant Exon 10 of 14 1 NM_001325.3 ENSP00000362063.2 P33240-1
CSTF2ENST00000415585.7 linkc.1200C>T p.Pro400Pro synonymous_variant Exon 11 of 15 1 ENSP00000387996.2 E7EWR4
CSTF2ENST00000475126.5 linkn.1089C>T non_coding_transcript_exon_variant Exon 10 of 14 5 ENSP00000432060.1 E9PID8

Frequencies

GnomAD3 genomes
AF:
0.0219
AC:
2449
AN:
111873
Hom.:
66
Cov.:
22
AF XY:
0.0195
AC XY:
664
AN XY:
34085
show subpopulations
Gnomad AFR
AF:
0.0752
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00914
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00840
Gnomad NFE
AF:
0.000414
Gnomad OTH
AF:
0.0139
GnomAD3 exomes
AF:
0.00635
AC:
1119
AN:
176296
Hom.:
35
AF XY:
0.00388
AC XY:
238
AN XY:
61282
show subpopulations
Gnomad AFR exome
AF:
0.0784
Gnomad AMR exome
AF:
0.00356
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000738
Gnomad SAS exome
AF:
0.000111
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000192
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.00247
AC:
2706
AN:
1095972
Hom.:
77
Cov.:
31
AF XY:
0.00196
AC XY:
710
AN XY:
361464
show subpopulations
Gnomad4 AFR exome
AF:
0.0793
Gnomad4 AMR exome
AF:
0.00482
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000149
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000163
Gnomad4 OTH exome
AF:
0.00606
GnomAD4 genome
AF:
0.0220
AC:
2466
AN:
111925
Hom.:
69
Cov.:
22
AF XY:
0.0197
AC XY:
673
AN XY:
34147
show subpopulations
Gnomad4 AFR
AF:
0.0756
Gnomad4 AMR
AF:
0.00913
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000414
Gnomad4 OTH
AF:
0.0138
Alfa
AF:
0.00852
Hom.:
76
Bravo
AF:
0.0251

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
7.5
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61741775; hg19: chrX-100087831; API