chr6-149377766-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001292034.3(TAB2):​c.103-252G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,202 control chromosomes in the GnomAD database, including 60,250 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.89 ( 60250 hom., cov: 32)

Consequence

TAB2
NM_001292034.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.268
Variant links:
Genes affected
TAB2 (HGNC:17075): (TGF-beta activated kinase 1 (MAP3K7) binding protein 2) The protein encoded by this gene is an activator of MAP3K7/TAK1, which is required for for the IL-1 induced activation of nuclear factor kappaB and MAPK8/JNK. This protein forms a kinase complex with TRAF6, MAP3K7 and TAB1, and it thus serves as an adaptor that links MAP3K7 and TRAF6. This protein, along with TAB1 and MAP3K7, also participates in the signal transduction induced by TNFSF11/RANKl through the activation of the receptor activator of NF-kappaB (TNFRSF11A/RANK), which may regulate the development and function of osteoclasts. Studies of the related mouse protein indicate that it functions to protect against liver damage caused by chemical stressors. Mutations in this gene cause congenital heart defects, multiple types, 2 (CHTD2). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BP6
Variant 6-149377766-G-T is Benign according to our data. Variant chr6-149377766-G-T is described in ClinVar as [Benign]. Clinvar id is 1295410.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TAB2NM_001292034.3 linkuse as main transcriptc.103-252G>T intron_variant ENST00000637181.2 NP_001278963.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TAB2ENST00000637181.2 linkuse as main transcriptc.103-252G>T intron_variant 1 NM_001292034.3 ENSP00000490618 P1Q9NYJ8-1

Frequencies

GnomAD3 genomes
AF:
0.890
AC:
135312
AN:
152084
Hom.:
60200
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.887
Gnomad AMI
AF:
0.823
Gnomad AMR
AF:
0.898
Gnomad ASJ
AF:
0.940
Gnomad EAS
AF:
0.886
Gnomad SAS
AF:
0.915
Gnomad FIN
AF:
0.872
Gnomad MID
AF:
0.962
Gnomad NFE
AF:
0.888
Gnomad OTH
AF:
0.908
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.890
AC:
135418
AN:
152202
Hom.:
60250
Cov.:
32
AF XY:
0.889
AC XY:
66183
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.887
Gnomad4 AMR
AF:
0.898
Gnomad4 ASJ
AF:
0.940
Gnomad4 EAS
AF:
0.887
Gnomad4 SAS
AF:
0.913
Gnomad4 FIN
AF:
0.872
Gnomad4 NFE
AF:
0.888
Gnomad4 OTH
AF:
0.909
Alfa
AF:
0.880
Hom.:
2826
Bravo
AF:
0.893
Asia WGS
AF:
0.887
AC:
3072
AN:
3462

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 testingGeneDxSep 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.30
DANN
Benign
0.19

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: rs6916134; hg19: chr6-149698902; API