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GeneBe

7-101087831-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_030961.3(TRIM56):c.519C>T(p.Pro173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,603,680 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 2 hom. )

Consequence

TRIM56
NM_030961.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -9.71
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 Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-101087831-C-T is Benign according to our data. Variant chr7-101087831-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657853.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-9.71 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIM56NM_030961.3 linkuse as main transcriptc.519C>T p.Pro173= synonymous_variant 3/3 ENST00000306085.11
TRIM56XM_011516589.4 linkuse as main transcriptc.519C>T p.Pro173= synonymous_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM56ENST00000306085.11 linkuse as main transcriptc.519C>T p.Pro173= synonymous_variant 3/31 NM_030961.3 P1Q9BRZ2-1
TRIM56ENST00000412507.1 linkuse as main transcriptc.519C>T p.Pro173= synonymous_variant 3/41

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00161
AC:
245
AN:
152164
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00222
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.000865
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00292
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00147
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00118
AC:
277
AN:
234890
Hom.:
0
AF XY:
0.00117
AC XY:
151
AN XY:
128820
show subpopulations
Gnomad AFR exome
AF:
0.00273
Gnomad AMR exome
AF:
0.000207
Gnomad ASJ exome
AF:
0.000629
Gnomad EAS exome
AF:
0.00119
Gnomad SAS exome
AF:
0.0000336
Gnomad FIN exome
AF:
0.00225
Gnomad NFE exome
AF:
0.00146
Gnomad OTH exome
AF:
0.00138
GnomAD4 exome
AF:
0.00143
AC:
2079
AN:
1451398
Hom.:
2
Cov.:
29
AF XY:
0.00136
AC XY:
983
AN XY:
721498
show subpopulations
Gnomad4 AFR exome
AF:
0.00156
Gnomad4 AMR exome
AF:
0.000339
Gnomad4 ASJ exome
AF:
0.000465
Gnomad4 EAS exome
AF:
0.00149
Gnomad4 SAS exome
AF:
0.0000701
Gnomad4 FIN exome
AF:
0.00197
Gnomad4 NFE exome
AF:
0.00157
Gnomad4 OTH exome
AF:
0.00152
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00166
AC:
253
AN:
152282
Hom.:
1
Cov.:
33
AF XY:
0.00171
AC XY:
127
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.00241
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.000865
Gnomad4 EAS
AF:
0.00213
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00292
Gnomad4 NFE
AF:
0.00147
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00135
Hom.:
0
Bravo
AF:
0.00139
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023TRIM56: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
0.056
Dann
Benign
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs145410552; hg19: chr7-100731112; COSMIC: COSV60162143; COSMIC: COSV60162143; API