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GeneBe

3-49829151-T-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005879.3(TRAIP):c.1362A>C(p.Thr454=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 1,614,094 control chromosomes in the GnomAD database, including 23,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2804 hom., cov: 32)
Exomes 𝑓: 0.16 ( 20762 hom. )

Consequence

TRAIP
NM_005879.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.72
Variant links:
Genes affected
TRAIP (HGNC:30764): (TRAF interacting protein) This gene encodes a protein that contains an N-terminal RING finger motif and a putative coiled-coil domain. A similar murine protein interacts with TNFR-associated factor 1 (TRAF1), TNFR-associated factor 2 (TRAF2), and cylindromatosis. The interaction with TRAF2 inhibits TRAF2-mediated nuclear factor kappa-B, subunit 1 activation that is required for cell activation and protection against apoptosis. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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 3-49829151-T-G is Benign according to our data. Variant chr3-49829151-T-G is described in ClinVar as [Benign]. Clinvar id is 1098863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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=1.72 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 = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAIPNM_005879.3 linkuse as main transcriptc.1362A>C p.Thr454= synonymous_variant 15/15 ENST00000331456.7
TRAIPXM_017005526.2 linkuse as main transcriptc.1065A>C p.Thr355= synonymous_variant 12/12
TRAIPXM_047447240.1 linkuse as main transcriptc.834A>C p.Thr278= synonymous_variant 10/10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAIPENST00000331456.7 linkuse as main transcriptc.1362A>C p.Thr454= synonymous_variant 15/151 NM_005879.3 P1
TRAIPENST00000491060.1 linkuse as main transcriptn.516A>C non_coding_transcript_exon_variant 2/23
TRAIPENST00000473195.5 linkuse as main transcriptc.*535A>C 3_prime_UTR_variant, NMD_transcript_variant 10/103

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.180
AC:
27315
AN:
152106
Hom.:
2790
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.259
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.141
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.00846
Gnomad SAS
AF:
0.0562
Gnomad FIN
AF:
0.0893
Gnomad MID
AF:
0.241
Gnomad NFE
AF:
0.176
Gnomad OTH
AF:
0.191
GnomAD3 exomes
AF:
0.136
AC:
34264
AN:
251294
Hom.:
2945
AF XY:
0.135
AC XY:
18302
AN XY:
135816
show subpopulations
Gnomad AFR exome
AF:
0.261
Gnomad AMR exome
AF:
0.0885
Gnomad ASJ exome
AF:
0.156
Gnomad EAS exome
AF:
0.00500
Gnomad SAS exome
AF:
0.0565
Gnomad FIN exome
AF:
0.0905
Gnomad NFE exome
AF:
0.182
Gnomad OTH exome
AF:
0.157
GnomAD4 exome
AF:
0.162
AC:
236292
AN:
1461870
Hom.:
20762
Cov.:
33
AF XY:
0.159
AC XY:
115427
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.263
Gnomad4 AMR exome
AF:
0.0941
Gnomad4 ASJ exome
AF:
0.154
Gnomad4 EAS exome
AF:
0.00252
Gnomad4 SAS exome
AF:
0.0569
Gnomad4 FIN exome
AF:
0.0996
Gnomad4 NFE exome
AF:
0.178
Gnomad4 OTH exome
AF:
0.164
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.180
AC:
27351
AN:
152224
Hom.:
2804
Cov.:
32
AF XY:
0.173
AC XY:
12882
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.259
Gnomad4 AMR
AF:
0.141
Gnomad4 ASJ
AF:
0.154
Gnomad4 EAS
AF:
0.00829
Gnomad4 SAS
AF:
0.0559
Gnomad4 FIN
AF:
0.0893
Gnomad4 NFE
AF:
0.176
Gnomad4 OTH
AF:
0.189
Alfa
AF:
0.163
Hom.:
1153
Bravo
AF:
0.189
Asia WGS
AF:
0.0530
AC:
185
AN:
3478
EpiCase
AF:
0.183
EpiControl
AF:
0.188

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingInvitaeJan 31, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 05, 2021- -
Seckel syndrome 9 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabMay 18, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
4.3
Dann
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs35129566; hg19: chr3-49866584; COSMIC: COSV58914413; COSMIC: COSV58914413; API