Genetic Variant TCEAL3:p.Gln191Gln (chrX-103609637-G-A) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP7

The NM_032926.3(TCEAL3):c.573G>A(p.Gln191Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0000090 ( 0 hom., 1 hem., cov: 23)

Exomes 𝑓: 0.00017 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

TCEAL3
NM_032926.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500

Publications

2 publications found

Variant links:

Genes affected

TCEAL3 (HGNC:28247): (transcription elongation factor A like 3) 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. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]

TCEAL3 links:

ENSG00000304280 (HGNC:):

ENSG00000304280 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP7

Synonymous conserved (PhyloP=-0.05 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032926.3. 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
	TCEAL3	NM_032926.3	MANE Select	c.573G>A	p.Gln191Gln	synonymous	Exon 3 of 3	NP_116315.1	Q969E4
	TCEAL3	NM_001006933.2		c.573G>A	p.Gln191Gln	synonymous	Exon 3 of 3	NP_001006934.1	Q969E4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TCEAL3	ENST00000372627.10	TSL:1 MANE Select	c.573G>A	p.Gln191Gln	synonymous	Exon 3 of 3	ENSP00000361710.5	Q969E4
TCEAL3	ENST00000243286.7	TSL:1	c.573G>A	p.Gln191Gln	synonymous	Exon 3 of 3	ENSP00000243286.3	Q969E4
TCEAL3	ENST00000372628.5	TSL:5	c.573G>A	p.Gln191Gln	synonymous	Exon 3 of 3	ENSP00000361711.1	Q969E4

Frequencies

GnomAD3 genomes

AF:

0.00000896

AC:

AN:

111613

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000189

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.399

AC:

36457

AN:

91305

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.342

Gnomad AMR exome

AF:

0.403

Gnomad ASJ exome

AF:

0.443

Gnomad EAS exome

AF:

0.314

Gnomad FIN exome

AF:

0.490

Gnomad NFE exome

AF:

0.408

Gnomad OTH exome

AF:

0.364

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000165

AC:

145

AN:

876195

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

275081

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000229

AC:

AN:

21827

American (AMR)

AF:

0.00

AC:

AN:

31797

Ashkenazi Jewish (ASJ)

AF:

0.000120

AC:

AN:

16677

East Asian (EAS)

AF:

0.0000706

AC:

AN:

28324

South Asian (SAS)

AF:

0.0000863

AC:

AN:

46334

European-Finnish (FIN)

AF:

0.0000815

AC:

AN:

36804

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3121

European-Non Finnish (NFE)

AF:

0.000195

AC:

127

AN:

652692

Other (OTH)

AF:

0.0000518

AC:

AN:

38619

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.235

Heterozygous variant carriers

111

139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000896

AC:

AN:

111613

Hom.:

Cov.:

AF XY:

0.0000296

AC XY:

AN XY:

33799

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30696

American (AMR)

AF:

0.00

AC:

AN:

10581

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2639

East Asian (EAS)

AF:

0.00

AC:

AN:

3536

South Asian (SAS)

AF:

0.00

AC:

AN:

2665

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6057

Middle Eastern (MID)

AF:

0.00

AC:

AN:

233

European-Non Finnish (NFE)

AF:

0.0000189

AC:

AN:

53023

Other (OTH)

AF:

0.00

AC:

AN:

1498

Alfa

AF:

0.185

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

2.0

(source)

DANN

Benign

0.64

PhyloP100

-0.050

Mutation Taster

=100/0

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over