10-70781091-C-G

Variant names:

• chr10-70781091-C-G
• rs1880055
• NM_001318241.2:c.277+710G>C

Variant summary

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

The NM_001318241.2(TBATA):​c.277+710G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,024 control chromosomes in the GnomAD database, including 11,030 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 0.38 (11030 hom., cov: 32)
• Consequence: TBATA NM_001318241.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 6 publications found

Genes affected

TBATA (HGNC:23511): (thymus, brain and testes associated) This gene encodes a protein that regulates thymic epithelial cell proliferation and thymus size. It has been identified as a ligand for the class I human leukocyte antigen (HLA-I) in thymus. Studies of the orthologous mouse protein suggest that it may also play a role in spermatid differentiation, as well as in neuronal morphogenesis and synaptic plasticity. Polymorphisms in this gene are associated with susceptibility for multiple sclerosis (MS). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBATA	NM_001318241.2	c.277+710G>C		intron_variant	Intron 4 of 10	ENST00000456372.4	NP_001305170.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBATA	ENST00000456372.4	c.277+710G>C		intron_variant	Intron 4 of 10	1	NM_001318241.2	ENSP00000400224.3
TBATA	ENST00000692183.1	c.277+710G>C		intron_variant	Intron 4 of 10			ENSP00000509602.1

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57722 AN: 151904 Hom.: 11014 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.380 AC: 57786 AN: 152024 Hom.: 11030 Cov.: 32 AF XY: 0.379 AC XY: 28145 AN XY: 74314

African (AFR) AF: 0.357 AC: 14812 AN: 41444

American (AMR) AF: 0.417 AC: 6381 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2235 AN: 5146

South Asian (SAS) AF: 0.456 AC: 2195 AN: 4816

European-Finnish (FIN) AF: 0.309 AC: 3269 AN: 10576

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26177 AN: 67960

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.376 Hom.: 1321

Bravo AF: 0.385

Asia WGS AF: 0.484 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.56
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1880055; hg19: chr10-72540847;