7-88219980-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_003130.4(SRI):c.47G>T(p.Gly16Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SRI
NM_003130.4 missense
NM_003130.4 missense
Scores
3
13
2
Clinical Significance
Conservation
PhyloP100: 3.98
Publications
0 publications found
Genes affected
SRI (HGNC:11292): (sorcin) This gene encodes a calcium-binding protein with multiple E-F hand domains that relocates from the cytoplasm to the sarcoplasmic reticulum in response to elevated calcium levels. In addition to regulating intracellular calcium homeostasis it also modulates excitation-contraction coupling in the heart. Alternative splicing results in multiple transcript variants encoding distinct proteins. Multiple pseudogenes exist for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.785
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003130.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| SRI | TSL:1 MANE Select | c.47G>T | p.Gly16Val | missense | Exon 1 of 8 | ENSP00000265729.3 | P30626-1 | ||
| SRI | TSL:1 | n.81G>T | non_coding_transcript_exon | Exon 1 of 6 | |||||
| SRI | c.47G>T | p.Gly16Val | missense | Exon 1 of 8 | ENSP00000549619.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1387946Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 685326
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1387946
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
685326
African (AFR)
AF:
AC:
0
AN:
30576
American (AMR)
AF:
AC:
0
AN:
35930
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24974
East Asian (EAS)
AF:
AC:
0
AN:
35460
South Asian (SAS)
AF:
AC:
0
AN:
78750
European-Finnish (FIN)
AF:
AC:
0
AN:
41482
Middle Eastern (MID)
AF:
AC:
0
AN:
4274
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1078776
Other (OTH)
AF:
AC:
0
AN:
57724
GnomAD4 genome
GnomAD4 genome
Cov.:
33
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
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
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
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