rs7758080

Variant names:

• chr6-149255943-A-G
• rs7758080
• NM_001292035.3:c.6+37167A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-149255943-A-G
• chr6-149255943-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001292035.3(TAB2):​c.6+37167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,108 control chromosomes in the GnomAD database, including 7,830 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 0.31 (7830 hom., cov: 32)
• Consequence: TAB2 NM_001292035.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 25 publications found

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]

TAB2-AS1 (HGNC:53508): (TAB2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001292035.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAB2	NM_001292035.3		c.6+37167A>G		intron	N/A	NP_001278964.1
	TAB2-AS1	NR_149096.1		n.168+1441T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAB2	ENST00000606202.1	TSL:4	c.-121+37167A>G		intron	N/A	ENSP00000476139.1
	TAB2-AS1	ENST00000424421.3	TSL:5	n.174+1441T>C		intron	N/A
	TAB2-AS1	ENST00000637865.1	TSL:5	n.161-603T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47671 AN: 151990 Hom.: 7823 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.314 AC: 47710 AN: 152108 Hom.: 7830 Cov.: 32 AF XY: 0.312 AC XY: 23213 AN XY: 74374

African (AFR) AF: 0.400 AC: 16578 AN: 41456

American (AMR) AF: 0.271 AC: 4149 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2135 AN: 5166

South Asian (SAS) AF: 0.309 AC: 1492 AN: 4832

European-Finnish (FIN) AF: 0.219 AC: 2315 AN: 10594

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18440 AN: 67992

Other (OTH) AF: 0.338 AC: 713 AN: 2110

Alfa AF: 0.292 Hom.: 13247

Bravo AF: 0.325

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7758080; hg19: chr6-149577079;