dbSNP rs360712: TEX12:p.Arg12Arg (chr11-112169304-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_031275.4(TEX12):c.36A>G(p.Arg12Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,611,342 control chromosomes in the GnomAD database, including 50,407 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 0.21 ( 3810 hom., cov: 32)

Exomes 𝑓: 0.25 ( 46597 hom. )

Consequence

TEX12
NM_031275.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.47

Publications

23 publications found

Variant links:

Genes affected

TEX12 (HGNC:11734): (testis expressed 12) This gene is similar to a mouse gene that is expressed in the testis. [provided by RefSeq, Jul 2008]

TEX12 links:

ENSG00000255292 (HGNC:):

ENSG00000255292 links:

ENSG00000254638 (HGNC:58436):

ENSG00000254638 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP7

Synonymous conserved (PhyloP=1.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX12	NM_031275.4 link	c.36A>G	p.Arg12Arg	synonymous_variant	Exon 2 of 5	ENST00000280358.5	NP_112565.1	Q9BXU0A0A024R3E7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX12	ENST00000280358.5 link	c.36A>G	p.Arg12Arg	synonymous_variant	Exon 2 of 5	1	NM_031275.4	ENSP00000280358.4		Q9BXU0
ENSG00000255292	ENST00000532699.1 link	n.315-1115A>G		intron_variant	Intron 3 of 5	3		ENSP00000456434.1		H3BRW5

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31419

AN:

152038

Hom.:

3809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0842

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.212

Gnomad FIN

AF:

0.285

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.208

GnomAD2 exomes

AF:

0.242

AC:

60892

AN:

251194

AF XY:

0.244

show subpopulations

Gnomad AFR exome

AF:

0.0808

Gnomad AMR exome

AF:

0.300

Gnomad ASJ exome

AF:

0.243

Gnomad EAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.280

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.250

AC:

364210

AN:

1459186

Hom.:

46597

Cov.:

AF XY:

0.250

AC XY:

181215

AN XY:

725998

show subpopulations

African (AFR)

AF:

0.0778

AC:

2604

AN:

33456

American (AMR)

AF:

0.298

AC:

13309

AN:

44654

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

6368

AN:

26098

East Asian (EAS)

AF:

0.127

AC:

5050

AN:

39674

South Asian (SAS)

AF:

0.226

AC:

19438

AN:

86140

European-Finnish (FIN)

AF:

0.282

AC:

15066

AN:

53394

Middle Eastern (MID)

AF:

0.199

AC:

1148

AN:

5764

European-Non Finnish (NFE)

AF:

0.259

AC:

286952

AN:

1109696

Other (OTH)

AF:

0.237

AC:

14275

AN:

60310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

12127

24254

36380

48507

60634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9572

19144

28716

38288

47860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.206

AC:

31410

AN:

152156

Hom.:

3810

Cov.:

AF XY:

0.209

AC XY:

15518

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0840

AC:

3491

AN:

41550

American (AMR)

AF:

0.266

AC:

4067

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

871

AN:

3470

East Asian (EAS)

AF:

0.125

AC:

648

AN:

5166

South Asian (SAS)

AF:

0.211

AC:

1018

AN:

4822

European-Finnish (FIN)

AF:

0.285

AC:

3009

AN:

10570

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.259

AC:

17615

AN:

67970

Other (OTH)

AF:

0.205

AC:

434

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1253

2506

3760

5013

6266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.240

Hom.:

10192

Bravo

AF:

0.200

Asia WGS

AF:

0.174

AC:

606

AN:

3478

EpiCase

AF:

0.249

EpiControl

AF:

0.253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

1.5

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over