7-101087796-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_030961.3(TRIM56):​c.484C>G​(p.Arg162Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R162W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

TRIM56
NM_030961.3 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800
Variant links:
Genes affected
TRIM56 (HGNC:19028): (tripartite motif containing 56) Enables RNA binding activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of macromolecule metabolic process; and protein K63-linked ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in chromatin and nucleoplasm. [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 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30447203).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIM56NM_030961.3 linkc.484C>G p.Arg162Gly missense_variant Exon 3 of 3 ENST00000306085.11 NP_112223.1 Q9BRZ2-1
TRIM56XM_011516589.4 linkc.484C>G p.Arg162Gly missense_variant Exon 2 of 2 XP_011514891.1 Q9BRZ2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM56ENST00000306085.11 linkc.484C>G p.Arg162Gly missense_variant Exon 3 of 3 1 NM_030961.3 ENSP00000305161.6 Q9BRZ2-1
TRIM56ENST00000412507.1 linkc.484C>G p.Arg162Gly missense_variant Exon 3 of 4 1 ENSP00000404186.1 C9JI91

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000206
AC:
3
AN:
1454040
Hom.:
0
Cov.:
29
AF XY:
0.00000277
AC XY:
2
AN XY:
723186
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.84
BayesDel_addAF
Benign
-0.022
T
BayesDel_noAF
Benign
-0.27
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.25
T;.
Eigen
Uncertain
0.43
Eigen_PC
Uncertain
0.38
FATHMM_MKL
Benign
0.24
N
LIST_S2
Benign
0.77
T;T
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.30
T;T
MetaSVM
Benign
-0.72
T
MutationAssessor
Uncertain
2.0
M;.
PrimateAI
Uncertain
0.75
T
PROVEAN
Uncertain
-4.2
D;D
REVEL
Benign
0.16
Sift
Benign
0.40
T;D
Sift4G
Uncertain
0.016
D;D
Polyphen
0.99
D;D
Vest4
0.30
MutPred
0.45
Loss of helix (P = 0.0558);Loss of helix (P = 0.0558);
MVP
0.69
MPC
1.4
ClinPred
0.92
D
GERP RS
4.0
Varity_R
0.33
gMVP
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-100731077; API