12-112130551-C-A

Variant summary

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

The NM_006700.3(TRAFD1):​c.29C>A​(p.Thr10Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

TRAFD1
NM_006700.3 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.03
Variant links:
Genes affected
TRAFD1 (HGNC:24808): (TRAF-type zinc finger domain containing 1) The innate immune system confers host defense against viral and microbial infection, and TRAFD1 is a negative feedback regulator that controls excessive immune responses (Sanada et al., 2008 [PubMed 18849341]).[supplied by OMIM, Dec 2009]

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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=0.25075805).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRAFD1NM_006700.3 linkc.29C>A p.Thr10Asn missense_variant Exon 2 of 12 ENST00000412615.7 NP_006691.1 O14545-1A0A024RBK4
TRAFD1NM_001143906.2 linkc.29C>A p.Thr10Asn missense_variant Exon 2 of 12 NP_001137378.1 O14545-1A0A024RBK4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRAFD1ENST00000412615.7 linkc.29C>A p.Thr10Asn missense_variant Exon 2 of 12 1 NM_006700.3 ENSP00000396526.2 O14545-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 24, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.29C>A (p.T10N) alteration is located in exon 2 (coding exon 1) of the TRAFD1 gene. This alteration results from a C to A substitution at nucleotide position 29, causing the threonine (T) at amino acid position 10 to be replaced by an asparagine (N). 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
0.15
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.53
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Uncertain
0.58
D;T;D;T
Eigen
Benign
0.12
Eigen_PC
Benign
0.049
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Benign
0.71
.;T;T;T
M_CAP
Benign
0.0073
T
MetaRNN
Benign
0.25
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.8
L;.;L;.
PrimateAI
Benign
0.44
T
PROVEAN
Uncertain
-2.6
D;D;D;D
REVEL
Benign
0.14
Sift
Uncertain
0.021
D;T;D;D
Sift4G
Uncertain
0.0080
D;T;D;D
Polyphen
0.99
D;.;D;D
Vest4
0.37
MutPred
0.40
Gain of helix (P = 0.0325);Gain of helix (P = 0.0325);Gain of helix (P = 0.0325);Gain of helix (P = 0.0325);
MVP
0.31
MPC
0.37
ClinPred
0.74
D
GERP RS
4.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.080
gMVP
0.45

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: chr12-112568355; API