dbSNP rs5944858: TCEAL2:p.Arg205Arg (chrX-102127445-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_080390.4(TCEAL2):c.615G>A(p.Arg205Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,199,996 control chromosomes in the GnomAD database, including 10,478 homozygotes. There are 58,806 hemizygotes in GnomAD. 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 0.12 ( 820 hom., 3668 hem., cov: 23)

Exomes 𝑓: 0.16 ( 9658 hom. 55138 hem. )

Consequence

TCEAL2
NM_080390.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.742

Publications

5 publications found

Variant links:

Genes affected

TCEAL2 (HGNC:29818): (transcription elongation factor A like 2) This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. [provided by RefSeq, Jul 2008]

TCEAL2 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=-0.66).

BP7

Synonymous conserved (PhyloP=0.742 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEAL2	NM_080390.4 link	c.615G>A	p.Arg205Arg	synonymous_variant	Exon 3 of 3	ENST00000372780.6	NP_525129.1	Q9H3H9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TCEAL2	ENST00000372780.6 link	c.615G>A	p.Arg205Arg	synonymous_variant	Exon 3 of 3	1	NM_080390.4	ENSP00000361866.1	Q9H3H9
TCEAL2	ENST00000329035.2 link	c.615G>A	p.Arg205Arg	synonymous_variant	Exon 3 of 3	5		ENSP00000332359.2	Q9H3H9
TCEAL2	ENST00000651085.1 link	n.153+1000G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

13251

AN:

110898

Hom.:

820

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0313

Gnomad AMI

AF:

0.0498

Gnomad AMR

AF:

0.0971

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.00225

Gnomad SAS

AF:

0.0357

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.157

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.118

GnomAD2 exomes

AF:

0.0907

AC:

14545

AN:

160391

AF XY:

0.0858

show subpopulations

Gnomad AFR exome

AF:

0.0199

Gnomad AMR exome

AF:

0.0464

Gnomad ASJ exome

AF:

0.0983

Gnomad EAS exome

AF:

0.000902

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.156

AC:

169580

AN:

1089045

Hom.:

9658

Cov.:

AF XY:

0.155

AC XY:

55138

AN XY:

356127

show subpopulations

African (AFR)

AF:

0.0265

AC:

686

AN:

25872

American (AMR)

AF:

0.0678

AC:

2272

AN:

33525

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

2861

AN:

18737

East Asian (EAS)

AF:

0.000331

AC:

AN:

30188

South Asian (SAS)

AF:

0.0499

AC:

2576

AN:

51673

European-Finnish (FIN)

AF:

0.202

AC:

8150

AN:

40284

Middle Eastern (MID)

AF:

0.203

AC:

815

AN:

4009

European-Non Finnish (NFE)

AF:

0.174

AC:

145665

AN:

839084

Other (OTH)

AF:

0.143

AC:

6545

AN:

45673

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

5381

10762

16142

21523

26904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5116

10232

15348

20464

25580

<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:

0.119

AC:

13248

AN:

110951

Hom.:

820

Cov.:

AF XY:

0.111

AC XY:

3668

AN XY:

33191

show subpopulations

African (AFR)

AF:

0.0312

AC:

955

AN:

30610

American (AMR)

AF:

0.0969

AC:

1021

AN:

10532

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

399

AN:

2628

East Asian (EAS)

AF:

0.00226

AC:

AN:

3544

South Asian (SAS)

AF:

0.0358

AC:

AN:

2628

European-Finnish (FIN)

AF:

0.199

AC:

1163

AN:

5847

Middle Eastern (MID)

AF:

0.153

AC:

AN:

215

European-Non Finnish (NFE)

AF:

0.178

AC:

9364

AN:

52743

Other (OTH)

AF:

0.116

AC:

177

AN:

1521

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

419

838

1257

1676

2095

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.148

Hom.:

1278

Bravo

AF:

0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

7.7

(source)

DANN

Benign

0.61

PhyloP100

0.74

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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