NM_002068.4:c.212C>T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_002068.4(GNA15):c.212C>T(p.Ser71Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000278 in 1,438,828 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
GNA15
NM_002068.4 missense
NM_002068.4 missense
Scores
9
6
Clinical Significance
Conservation
PhyloP100: 4.05
Publications
0 publications found
Genes affected
GNA15 (HGNC:4383): (G protein subunit alpha 15) Enables G protein-coupled receptor binding activity. Involved in positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway. Predicted to be located in plasma membrane. Predicted to be part of heterotrimeric G-protein complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002068.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| GNA15 | TSL:1 MANE Select | c.212C>T | p.Ser71Leu | missense | Exon 2 of 7 | ENSP00000262958.2 | P30679 | ||
| GNA15-DT | TSL:2 | n.1292G>A | non_coding_transcript_exon | Exon 2 of 4 | |||||
| GNA15 | TSL:3 | n.*242C>T | non_coding_transcript_exon | Exon 3 of 5 | ENSP00000467256.1 | K7EP74 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 0.00000278 AC: 4AN: 1438828Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1AN XY: 713610 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1438828
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
713610
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33056
American (AMR)
AF:
AC:
2
AN:
41280
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
25692
East Asian (EAS)
AF:
AC:
0
AN:
38726
South Asian (SAS)
AF:
AC:
0
AN:
83154
European-Finnish (FIN)
AF:
AC:
0
AN:
50828
Middle Eastern (MID)
AF:
AC:
0
AN:
5740
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1100848
Other (OTH)
AF:
AC:
0
AN:
59504
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
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
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
D
Vest4
MutPred
Gain of stability (P = 0.0174)
MVP
MPC
ClinPred
D
GERP RS
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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