chr16-11254845-A-C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4
The NM_003745.2(SOCS1):c.634T>G(p.Ter212Glyext*?) variant causes a stop lost change. The variant allele was found at a frequency of 0.000000756 in 1,323,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 7.6e-7 ( 0 hom. )
Consequence
SOCS1
NM_003745.2 stop_lost
NM_003745.2 stop_lost
Scores
1
2
3
Clinical Significance
Conservation
PhyloP100: 6.36
Publications
0 publications found
Genes affected
SOCS1 (HGNC:19383): (suppressor of cytokine signaling 1) This gene encodes a member of the STAT-induced STAT inhibitor (SSI), also known as suppressor of cytokine signaling (SOCS), family. SSI family members are cytokine-inducible negative regulators of cytokine signaling. The expression of this gene can be induced by a subset of cytokines, including IL2, IL3 erythropoietin (EPO), CSF2/GM-CSF, and interferon (IFN)-gamma. The protein encoded by this gene functions downstream of cytokine receptors, and takes part in a negative feedback loop to attenuate cytokine signaling. Knockout studies in mice suggested the role of this gene as a modulator of IFN-gamma action, which is required for normal postnatal growth and survival. [provided by RefSeq, Jul 2008]
RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Stoplost variant in NM_003745.2 Downstream stopcodon found after 269 codons.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_003745.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SOCS1 | NM_003745.2 | MANE Select | c.634T>G | p.Ter212Glyext*? | stop_lost | Exon 2 of 2 | NP_003736.1 | Q4JHT5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SOCS1 | ENST00000332029.4 | TSL:1 MANE Select | c.634T>G | p.Ter212Glyext*? | stop_lost | Exon 2 of 2 | ENSP00000329418.2 | O15524 | |
| RMI2 | ENST00000572173.1 | TSL:1 | c.-516+5067A>C | intron | N/A | ENSP00000461206.1 | Q96E14-2 | ||
| SOCS1 | ENST00000644787.2 | c.634T>G | p.Ter212Glyext*? | stop_lost | Exon 1 of 1 | ENSP00000496577.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 7.56e-7 AC: 1AN: 1323582Hom.: 0 Cov.: 32 AF XY: 0.00000153 AC XY: 1AN XY: 652760 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1323582
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
652760
show subpopulations
African (AFR)
AF:
AC:
0
AN:
25858
American (AMR)
AF:
AC:
0
AN:
20320
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18514
East Asian (EAS)
AF:
AC:
0
AN:
32520
South Asian (SAS)
AF:
AC:
0
AN:
64442
European-Finnish (FIN)
AF:
AC:
0
AN:
49388
Middle Eastern (MID)
AF:
AC:
0
AN:
5216
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1053392
Other (OTH)
AF:
AC:
0
AN:
53932
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
PhyloP100
Vest4
GERP RS
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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