NM_001318241.2:c.713G>A

Variant names:

• chr10-70775251-C-T
• rs2254174
• NM_001318241.2:c.713G>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001318241.2(TBATA):​c.713G>A​(p.Arg238Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 1,613,776 control chromosomes in the GnomAD database, including 611,632 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.83 (53203 hom., cov: 34)
  • Exomes 𝑓: 0.87 (558429 hom.)
• Consequence: TBATA NM_001318241.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 25 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318241.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBATA	NM_001318241.2	MANE Select	c.713G>A	p.Arg238Gln	missense	Exon 8 of 11	NP_001305170.1	A0A0A0MSR7
	TBATA	NM_001318242.2		c.710G>A	p.Arg237Gln	missense	Exon 8 of 11	NP_001305171.1	Q96M53-1
	TBATA	NM_152710.4		c.710G>A	p.Arg237Gln	missense	Exon 8 of 11	NP_689923.3	Q96M53-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBATA	ENST00000456372.4	TSL:1 MANE Select	c.713G>A	p.Arg238Gln	missense	Exon 8 of 11	ENSP00000400224.3	A0A0A0MSR7
	TBATA	ENST00000299290.5	TSL:1	c.710G>A	p.Arg237Gln	missense	Exon 8 of 11	ENSP00000299290.1	Q96M53-1
	TBATA	ENST00000692183.1		c.710G>A	p.Arg237Gln	missense	Exon 8 of 11	ENSP00000509602.1	Q96M53-1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126685 AN: 152112 Hom.: 53189 Cov.: 34

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.829

GnomAD2 exomes AF: 0.814 AC: 204576 AN: 251260 AF XY: 0.825

Gnomad AFR exome AF: 0.783

Gnomad AMR exome AF: 0.619

Gnomad ASJ exome AF: 0.870

Gnomad EAS exome AF: 0.583

Gnomad FIN exome AF: 0.844

Gnomad NFE exome AF: 0.897

Gnomad OTH exome AF: 0.837

GnomAD4 exome AF: 0.871 AC: 1272929 AN: 1461546 Hom.: 558429 Cov.: 49 AF XY: 0.871 AC XY: 633259 AN XY: 727056

African (AFR) AF: 0.779 AC: 26060 AN: 33468

American (AMR) AF: 0.633 AC: 28285 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 22780 AN: 26134

East Asian (EAS) AF: 0.590 AC: 23427 AN: 39686

South Asian (SAS) AF: 0.835 AC: 71975 AN: 86216

European-Finnish (FIN) AF: 0.847 AC: 45217 AN: 53378

Middle Eastern (MID) AF: 0.845 AC: 4874 AN: 5766

European-Non Finnish (NFE) AF: 0.898 AC: 998816 AN: 1111800

Other (OTH) AF: 0.853 AC: 51495 AN: 60384

GnomAD4 genome AF: 0.833 AC: 126742 AN: 152230 Hom.: 53203 Cov.: 34 AF XY: 0.827 AC XY: 61512 AN XY: 74420

African (AFR) AF: 0.785 AC: 32617 AN: 41546

American (AMR) AF: 0.733 AC: 11213 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3022 AN: 3470

East Asian (EAS) AF: 0.596 AC: 3067 AN: 5150

South Asian (SAS) AF: 0.830 AC: 4000 AN: 4818

European-Finnish (FIN) AF: 0.845 AC: 8963 AN: 10606

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61022 AN: 68028

Other (OTH) AF: 0.827 AC: 1746 AN: 2112

Alfa AF: 0.870 Hom.: 254908

Bravo AF: 0.817

TwinsUK AF: 0.896 AC: 3321

ALSPAC AF: 0.893 AC: 3442

ESP6500AA AF: 0.796 AC: 3507

ESP6500EA AF: 0.898 AC: 7724

ExAC AF: 0.824 AC: 100068

Asia WGS AF: 0.726 AC: 2526 AN: 3478

EpiCase AF: 0.893

EpiControl AF: 0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.049
BayesDel_addAF	Benign	-0.67	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	18
DANN	Benign	0.72
DEOGEN2	Benign	0.049	T
Eigen	Benign	-0.99
Eigen_PC	Benign	-0.68
FATHMM_MKL	Benign	0.044	N
LIST_S2	Benign	0.35	T
MetaRNN	Benign	5.6e-7	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	-1.9	N
PhyloP100		2.4
PrimateAI	Benign	0.44	T
PROVEAN	Benign	2.7	N
REVEL	Benign	0.11
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.12
MPC		0.10
ClinPred		0.0081	T
GERP RS		5.3
Varity_R		0.030
gMVP		0.058
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.36		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.36		Position offset: 19

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

Other links and lift over

dbSNP: rs2254174; hg19: chr10-72535007; COSMIC: COSV54719270; COSMIC: COSV54719270;