chr19-797517-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002819.5(PTBP1):c.8+12G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,520,180 control chromosomes in the GnomAD database, including 17,725 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2200 hom., cov: 32)
Exomes 𝑓: 0.15 ( 15525 hom. )
Consequence
PTBP1
NM_002819.5 intron
NM_002819.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.18
Genes affected
PTBP1 (HGNC:9583): (polypyrimidine tract binding protein 1) This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 19-797517-G-C is Benign according to our data. Variant chr19-797517-G-C is described in ClinVar as [Benign]. Clinvar id is 1301493.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTBP1 | NM_002819.5 | c.8+12G>C | intron_variant | Intron 1 of 14 | ENST00000356948.11 | NP_002810.1 | ||
PTBP1 | NM_031990.4 | c.8+12G>C | intron_variant | Intron 1 of 14 | NP_114367.1 | |||
PTBP1 | NM_031991.4 | c.8+12G>C | intron_variant | Intron 1 of 13 | NP_114368.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24656AN: 151364Hom.: 2188 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
24656
AN:
151364
Hom.:
Cov.:
32
Gnomad AFR
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GnomAD2 exomes AF: 0.167 AC: 22265AN: 133630 AF XY: 0.168 show subpopulations
GnomAD2 exomes
AF:
AC:
22265
AN:
133630
AF XY:
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GnomAD4 exome AF: 0.147 AC: 201211AN: 1368710Hom.: 15525 Cov.: 31 AF XY: 0.148 AC XY: 100471AN XY: 677810 show subpopulations
GnomAD4 exome
AF:
AC:
201211
AN:
1368710
Hom.:
Cov.:
31
AF XY:
AC XY:
100471
AN XY:
677810
Gnomad4 AFR exome
AF:
AC:
5760
AN:
28392
Gnomad4 AMR exome
AF:
AC:
6969
AN:
34710
Gnomad4 ASJ exome
AF:
AC:
4608
AN:
24198
Gnomad4 EAS exome
AF:
AC:
1237
AN:
31944
Gnomad4 SAS exome
AF:
AC:
13621
AN:
77844
Gnomad4 FIN exome
AF:
AC:
4008
AN:
38066
Gnomad4 NFE exome
AF:
AC:
154964
AN:
1072572
Gnomad4 Remaining exome
AF:
AC:
8972
AN:
56594
Heterozygous variant carriers
0
7956
15912
23868
31824
39780
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
5724
11448
17172
22896
28620
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.163 AC: 24700AN: 151470Hom.: 2200 Cov.: 32 AF XY: 0.162 AC XY: 12024AN XY: 74028 show subpopulations
GnomAD4 genome
AF:
AC:
24700
AN:
151470
Hom.:
Cov.:
32
AF XY:
AC XY:
12024
AN XY:
74028
Gnomad4 AFR
AF:
AC:
0.197091
AN:
0.197091
Gnomad4 AMR
AF:
AC:
0.205763
AN:
0.205763
Gnomad4 ASJ
AF:
AC:
0.186201
AN:
0.186201
Gnomad4 EAS
AF:
AC:
0.048714
AN:
0.048714
Gnomad4 SAS
AF:
AC:
0.176214
AN:
0.176214
Gnomad4 FIN
AF:
AC:
0.100996
AN:
0.100996
Gnomad4 NFE
AF:
AC:
0.148891
AN:
0.148891
Gnomad4 OTH
AF:
AC:
0.175238
AN:
0.175238
Heterozygous variant carriers
0
1036
2071
3107
4142
5178
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
272
544
816
1088
1360
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
480
AN:
3452
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
- -
Oct 20, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at