1-1312115-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_017871.6(INTS11):ā€‹c.1640C>Gā€‹(p.Pro547Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,424,658 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P547T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 25)
Exomes š‘“: 0.0000014 ( 0 hom. )

Consequence

INTS11
NM_017871.6 missense

Scores

2
2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.12
Variant links:
Genes affected
INTS11 (HGNC:26052): (integrator complex subunit 11) The Integrator complex contains at least 12 subunits and associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates the 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690). INTS11, or CPSF3L, is the catalytic subunit of the Integrator complex (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
INTS11NM_017871.6 linkc.1640C>G p.Pro547Arg missense_variant Exon 16 of 17 ENST00000435064.6 NP_060341.2 Q5TA45-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
INTS11ENST00000435064.6 linkc.1640C>G p.Pro547Arg missense_variant Exon 16 of 17 1 NM_017871.6 ENSP00000413493.2 Q5TA45-1

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD3 exomes
AF:
0.0000197
AC:
4
AN:
203216
Hom.:
0
AF XY:
0.0000367
AC XY:
4
AN XY:
109024
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000242
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000140
AC:
2
AN:
1424658
Hom.:
0
Cov.:
35
AF XY:
0.00000284
AC XY:
2
AN XY:
704208
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000512
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
25
Bravo
AF:
0.00000378
ExAC
AF:
0.0000253
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 12, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1640C>G (p.P547R) alteration is located in exon 16 (coding exon 16) of the CPSF3L gene. This alteration results from a C to G substitution at nucleotide position 1640, causing the proline (P) at amino acid position 547 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.10
T
BayesDel_noAF
Benign
-0.11
CADD
Benign
23
DANN
Benign
0.92
DEOGEN2
Benign
0.022
.;.;.;T;T;T;.;.;.
Eigen
Benign
-0.024
Eigen_PC
Benign
0.033
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
0.97
D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.028
D
MetaRNN
Uncertain
0.65
D;D;D;D;D;D;D;D;D
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.7
.;.;.;.;L;.;.;.;.
PrimateAI
Uncertain
0.75
T
PROVEAN
Benign
-0.48
N;N;.;.;N;N;.;N;N
REVEL
Benign
0.25
Sift
Benign
0.28
T;T;.;.;T;T;.;T;T
Sift4G
Benign
0.26
T;T;T;D;T;T;T;T;T
Polyphen
0.16, 0.28, 0.53, 0.25
.;.;.;.;B;B;.;P;B
Vest4
0.73
MutPred
0.44
.;.;.;.;Gain of catalytic residue at P547 (P = 0.0098);.;.;.;.;
MVP
0.84
MPC
0.032
ClinPred
0.21
T
GERP RS
4.0
Varity_R
0.50
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs755005813; hg19: chr1-1247495; API