Genetic Variant TBATA:p.Arg238Gln (chr10-70775251-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -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. 13/22 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.43

Variant links:

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]

TBATA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBATA	NM_001318241.2 link	c.713G>A	p.Arg238Gln	missense_variant	Exon 8 of 11	ENST00000456372.4	NP_001305170.1	A0A0A0MSR7B7ZMN5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBATA	ENST00000456372.4 link	c.713G>A	p.Arg238Gln	missense_variant	Exon 8 of 11	1	NM_001318241.2	ENSP00000400224.3		A0A0A0MSR7
TBATA	ENST00000692183.1 link	c.710G>A	p.Arg237Gln	missense_variant	Exon 8 of 11			ENSP00000509602.1		Q96M53-1

Frequencies

GnomAD3 genomes

AF:

0.833

AC:

126685

AN:

152112

Hom.:

53189

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.814

AC:

204576

AN:

251260

Hom.:

85102

AF XY:

0.825

AC XY:

112027

AN XY:

135812

show subpopulations

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 SAS exome

AF:

0.838

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.:

AF XY:

0.871

AC XY:

633259

AN XY:

727056

show subpopulations

Gnomad4 AFR exome

AF:

0.779

Gnomad4 AMR exome

AF:

0.633

Gnomad4 ASJ exome

AF:

0.872

Gnomad4 EAS exome

AF:

0.590

Gnomad4 SAS exome

AF:

0.835

Gnomad4 FIN exome

AF:

0.847

Gnomad4 NFE exome

AF:

0.898

Gnomad4 OTH exome

AF:

0.853

GnomAD4 genome

AF:

0.833

AC:

126742

AN:

152230

Hom.:

53203

Cov.:

AF XY:

0.827

AC XY:

61512

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.785

Gnomad4 AMR

AF:

0.733

Gnomad4 ASJ

AF:

0.871

Gnomad4 EAS

AF:

0.596

Gnomad4 SAS

AF:

0.830

Gnomad4 FIN

AF:

0.845

Gnomad4 NFE

AF:

0.897

Gnomad4 OTH

AF:

0.827

Alfa

AF:

0.874

Hom.:

139437

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 v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.049

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.72

DEOGEN2

Benign

0.049

T;.

Eigen

Benign

-0.99

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.044

LIST_S2

Benign

0.35

T;T

MetaRNN

Benign

5.6e-7

T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-1.9

N;.

PrimateAI

Benign

0.44

PROVEAN

Benign

2.7

N;.

REVEL

Benign

0.11

Sift

Benign

1.0

T;.

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;.

Vest4

0.12

MPC

0.10

ClinPred

0.0081

GERP RS

5.3

Varity_R

0.030

gMVP

0.058

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over