rs600739

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001292034.3(TAB2):​c.1939+704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,258 control chromosomes in the GnomAD database, including 1,740 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1740 hom., cov: 33)

Consequence

TAB2
NM_001292034.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAB2NM_001292034.3 linkuse as main transcriptc.1939+704A>G intron_variant ENST00000637181.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAB2ENST00000637181.2 linkuse as main transcriptc.1939+704A>G intron_variant 1 NM_001292034.3 P1Q9NYJ8-1

Frequencies

GnomAD3 genomes
AF:
0.122
AC:
18605
AN:
152140
Hom.:
1736
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0618
Gnomad AMI
AF:
0.00439
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.125
Gnomad EAS
AF:
0.513
Gnomad SAS
AF:
0.212
Gnomad FIN
AF:
0.121
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.126
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.122
AC:
18618
AN:
152258
Hom.:
1740
Cov.:
33
AF XY:
0.128
AC XY:
9557
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0619
Gnomad4 AMR
AF:
0.211
Gnomad4 ASJ
AF:
0.125
Gnomad4 EAS
AF:
0.513
Gnomad4 SAS
AF:
0.212
Gnomad4 FIN
AF:
0.121
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.112
Hom.:
159
Bravo
AF:
0.130
Asia WGS
AF:
0.327
AC:
1135
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.35
DANN
Benign
0.60

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: rs600739; hg19: chr6-149721024; API