8-144429287-G-A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_013432.5(TONSL):​c.3993C>T​(p.Ala1331Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,358,734 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000010 ( 0 hom. )

Consequence

TONSL
NM_013432.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.19
Variant links:
Genes affected
TONSL (HGNC:7801): (tonsoku like, DNA repair protein) The protein encoded by this gene is thought to be a negative regulator of NF-kappa-B mediated transcription. The encoded protein may bind NF-kappa-B complexes and trap them in the cytoplasm, preventing them from entering the nucleus and interacting with the DNA. Phosphorylation of this protein targets it for degradation by the ubiquitination pathway, which frees the NF-kappa-B complexes to enter the nucleus. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 8-144429287-G-A is Benign according to our data. Variant chr8-144429287-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2189380.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.19 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TONSLNM_013432.5 linkuse as main transcriptc.3993C>T p.Ala1331Ala synonymous_variant 26/26 ENST00000409379.8 NP_038460.4 Q96HA7-1
TONSLXM_011517048.3 linkuse as main transcriptc.3021C>T p.Ala1007Ala synonymous_variant 19/19 XP_011515350.1
TONSLXM_011517049.3 linkuse as main transcriptc.2985C>T p.Ala995Ala synonymous_variant 19/19 XP_011515351.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TONSLENST00000409379.8 linkuse as main transcriptc.3993C>T p.Ala1331Ala synonymous_variant 26/261 NM_013432.5 ENSP00000386239.3 Q96HA7-1
TONSLENST00000497613.2 linkuse as main transcriptn.6095C>T non_coding_transcript_exon_variant 17/172

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000247
AC:
3
AN:
121586
Hom.:
0
AF XY:
0.0000452
AC XY:
3
AN XY:
66366
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000672
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000103
AC:
14
AN:
1358734
Hom.:
0
Cov.:
30
AF XY:
0.0000135
AC XY:
9
AN XY:
666556
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:
0.0000259
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000104
Gnomad4 OTH exome
AF:
0.0000178
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

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 testingLabcorp Genetics (formerly Invitae), LabcorpMay 15, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
0.75
DANN
Benign
0.63
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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: rs1554878084; hg19: chr8-145654670; API