chr17-30179289-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_032141.4(NSRP1):c.500C>T(p.Ala167Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NSRP1
NM_032141.4 missense
NM_032141.4 missense
Scores
1
8
9
Clinical Significance
Conservation
PhyloP100: 2.12
Publications
0 publications found
Genes affected
NSRP1 (HGNC:25305): (nuclear speckle splicing regulatory protein 1) Enables mRNA binding activity. Involved in developmental process and regulation of alternative mRNA splicing, via spliceosome. Located in nuclear speck. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]
NSRP1 Gene-Disease associations (from GenCC):
- neurodevelopmental disorder with spasticity, seizures, and brain abnormalitiesInheritance: AR Classification: STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.40541118).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_032141.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NSRP1 | TSL:1 MANE Select | c.500C>T | p.Ala167Val | missense | Exon 5 of 7 | ENSP00000247026.5 | Q9H0G5 | ||
| NSRP1 | TSL:1 | c.338C>T | p.Ala113Val | missense | Exon 4 of 6 | ENSP00000477862.1 | A0A024QZ33 | ||
| NSRP1 | TSL:1 | n.*376C>T | non_coding_transcript_exon | Exon 5 of 7 | ENSP00000378303.4 | H7BYM1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1411500Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 701646
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1411500
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
701646
African (AFR)
AF:
AC:
0
AN:
31378
American (AMR)
AF:
AC:
0
AN:
37806
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24194
East Asian (EAS)
AF:
AC:
0
AN:
39236
South Asian (SAS)
AF:
AC:
0
AN:
76670
European-Finnish (FIN)
AF:
AC:
0
AN:
50836
Middle Eastern (MID)
AF:
AC:
0
AN:
5560
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1088158
Other (OTH)
AF:
AC:
0
AN:
57662
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of disorder (P = 0.0883)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.