16-270614-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_183337.3(RGS11):​c.1115G>A​(p.Arg372Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000274 in 1,607,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

RGS11
NM_183337.3 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.09
Variant links:
Genes affected
RGS11 (HGNC:9993): (regulator of G protein signaling 11) The protein encoded by this gene belongs to the RGS (regulator of G protein signaling) family. Members of the RGS family act as GTPase-activating proteins on the alpha subunits of heterotrimeric, signal-transducing G proteins. This protein inhibits signal transduction by increasing the GTPase activity of G protein alpha subunits, thereby driving them into their inactive GDP-bound form. Alternative splicing occurs at this locus and four transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Nov 2013]
FAM234A (HGNC:14163): (family with sequence similarity 234 member A) Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22916216).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RGS11NM_183337.3 linkc.1115G>A p.Arg372Gln missense_variant Exon 15 of 17 ENST00000397770.8 NP_899180.1 O94810-1Q4TT70

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RGS11ENST00000397770.8 linkc.1115G>A p.Arg372Gln missense_variant Exon 15 of 17 1 NM_183337.3 ENSP00000380876.3 O94810-1

Frequencies

GnomAD3 genomes
AF:
0.0000460
AC:
7
AN:
152142
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000507
AC:
12
AN:
236748
Hom.:
0
AF XY:
0.0000699
AC XY:
9
AN XY:
128844
show subpopulations
Gnomad AFR exome
AF:
0.0000677
Gnomad AMR exome
AF:
0.0000299
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000564
Gnomad SAS exome
AF:
0.0000341
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000565
Gnomad OTH exome
AF:
0.000348
GnomAD4 exome
AF:
0.0000254
AC:
37
AN:
1455836
Hom.:
0
Cov.:
32
AF XY:
0.0000263
AC XY:
19
AN XY:
723798
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000908
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000216
Gnomad4 OTH exome
AF:
0.0000999
GnomAD4 genome
AF:
0.0000460
AC:
7
AN:
152142
Hom.:
0
Cov.:
33
AF XY:
0.0000673
AC XY:
5
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.0000724
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000579
Hom.:
0
Bravo
AF:
0.0000756
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000745
AC:
9

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Sep 27, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1115G>A (p.R372Q) alteration is located in exon 15 (coding exon 15) of the RGS11 gene. This alteration results from a G to A substitution at nucleotide position 1115, causing the arginine (R) at amino acid position 372 to be replaced by a glutamine (Q). 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
0.080
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
19
DANN
Uncertain
1.0
DEOGEN2
Benign
0.15
T;.;.
Eigen
Benign
-0.33
Eigen_PC
Benign
-0.27
FATHMM_MKL
Benign
0.42
N
LIST_S2
Benign
0.84
T;T;T
M_CAP
Benign
0.036
D
MetaRNN
Benign
0.23
T;T;T
MetaSVM
Benign
-0.79
T
MutationAssessor
Benign
1.1
L;.;.
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-1.8
N;N;N
REVEL
Benign
0.024
Sift
Uncertain
0.010
D;D;D
Sift4G
Uncertain
0.025
D;D;T
Polyphen
0.32
B;.;B
Vest4
0.34
MVP
0.41
MPC
0.16
ClinPred
0.057
T
GERP RS
0.87
Varity_R
0.18
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs371409840; hg19: chr16-320613; COSMIC: COSV51452723; COSMIC: COSV51452723; API