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GeneBe

7-101087711-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_030961.3(TRIM56):c.399C>T(p.Asp133=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 1,586,064 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.018 ( 87 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 90 hom. )

Consequence

TRIM56
NM_030961.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.97
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 -15 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=-0.6).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-101087711-C-T is Benign according to our data. Variant chr7-101087711-C-T is described in ClinVar as [Benign]. Clinvar id is 778329.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=-3.97 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIM56NM_030961.3 linkuse as main transcriptc.399C>T p.Asp133= synonymous_variant 3/3 ENST00000306085.11
TRIM56XM_011516589.4 linkuse as main transcriptc.399C>T p.Asp133= synonymous_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM56ENST00000306085.11 linkuse as main transcriptc.399C>T p.Asp133= synonymous_variant 3/31 NM_030961.3 P1Q9BRZ2-1
TRIM56ENST00000412507.1 linkuse as main transcriptc.399C>T p.Asp133= synonymous_variant 3/41

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0183
AC:
2779
AN:
152118
Hom.:
82
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0629
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00785
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000265
Gnomad OTH
AF:
0.0153
GnomAD3 exomes
AF:
0.00465
AC:
1005
AN:
216298
Hom.:
24
AF XY:
0.00343
AC XY:
409
AN XY:
119088
show subpopulations
Gnomad AFR exome
AF:
0.0616
Gnomad AMR exome
AF:
0.00311
Gnomad ASJ exome
AF:
0.000129
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000333
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000330
Gnomad OTH exome
AF:
0.00399
GnomAD4 exome
AF:
0.00208
AC:
2986
AN:
1433828
Hom.:
90
Cov.:
29
AF XY:
0.00181
AC XY:
1284
AN XY:
710630
show subpopulations
Gnomad4 AFR exome
AF:
0.0676
Gnomad4 AMR exome
AF:
0.00368
Gnomad4 ASJ exome
AF:
0.0000819
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000288
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000240
Gnomad4 OTH exome
AF:
0.00469
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0185
AC:
2812
AN:
152236
Hom.:
87
Cov.:
33
AF XY:
0.0187
AC XY:
1392
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.0635
Gnomad4 AMR
AF:
0.00784
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000265
Gnomad4 OTH
AF:
0.0151
Alfa
AF:
0.00678
Hom.:
8
Bravo
AF:
0.0212
Asia WGS
AF:
0.00664
AC:
23
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
Cadd
Benign
0.91
Dann
Benign
0.82
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs36004695; hg19: chr7-100730992; API