Genetic Variant TCEAL6:p.Pro4Pro (chrX-102141320-G-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001006938.3(TCEAL6):c.12C>G(p.Pro4Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000484 in 1,205,144 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 202 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00040 ( 0 hom., 16 hem., cov: 24)

Exomes 𝑓: 0.00049 ( 0 hom. 186 hem. )

Consequence

TCEAL6
NM_001006938.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.70

Publications

1 publications found

Variant links:

Genes affected

TCEAL6 (HGNC:24553): (transcription elongation factor A like 6) Predicted to enable WW domain binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TCEAL6 links:

ENSG00000286794 (HGNC:):

ENSG00000286794 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant X-102141320-G-C is Benign according to our data. Variant chrX-102141320-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2661077.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.7 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 16 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001006938.3. 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
	TCEAL6	NM_001006938.3		c.12C>G	p.Pro4Pro	synonymous	Exon 3 of 3	NP_001006939.2	Q6IPX3-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TCEAL6	ENST00000372774.8	TSL:1	c.12C>G	p.Pro4Pro	synonymous	Exon 3 of 4	ENSP00000361860.4	Q6IPX3
TCEAL6	ENST00000372773.2	TSL:3	c.12C>G	p.Pro4Pro	synonymous	Exon 3 of 4	ENSP00000361859.2	Q6IPX3
ENSG00000286794	ENST00000828773.1		n.-224G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.000400

AC:

AN:

112618

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000646

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000931

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000365

Gnomad FIN

AF:

0.000323

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000732

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000385

AC:

AN:

174028

AF XY:

0.000246

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000381

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000255

Gnomad NFE exome

AF:

0.000771

Gnomad OTH exome

AF:

0.000468

GnomAD4 exome

AF:

0.000492

AC:

538

AN:

1092526

Hom.:

Cov.:

AF XY:

0.000517

AC XY:

186

AN XY:

359620

show subpopulations

African (AFR)

AF:

0.0000388

AC:

AN:

25804

American (AMR)

AF:

0.0000294

AC:

AN:

34001

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19108

East Asian (EAS)

AF:

0.00

AC:

AN:

30174

South Asian (SAS)

AF:

0.000171

AC:

AN:

52657

European-Finnish (FIN)

AF:

0.000545

AC:

AN:

40402

Middle Eastern (MID)

AF:

0.000244

AC:

AN:

4092

European-Non Finnish (NFE)

AF:

0.000583

AC:

490

AN:

840493

Other (OTH)

AF:

0.000306

AC:

AN:

45795

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.000400

AC:

AN:

112618

Hom.:

Cov.:

AF XY:

0.000460

AC XY:

AN XY:

34786

show subpopulations

African (AFR)

AF:

0.0000646

AC:

AN:

30979

American (AMR)

AF:

0.0000931

AC:

AN:

10746

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2653

East Asian (EAS)

AF:

0.00

AC:

AN:

3573

South Asian (SAS)

AF:

0.000365

AC:

AN:

2737

European-Finnish (FIN)

AF:

0.000323

AC:

AN:

6195

Middle Eastern (MID)

AF:

0.00

AC:

AN:

240

European-Non Finnish (NFE)

AF:

0.000732

AC:

AN:

53289

Other (OTH)

AF:

0.00

AC:

AN:

1521

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

Alfa

AF:

0.000564

Hom.:

Bravo

AF:

0.000431

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.2

(source)

DANN

Benign

0.61

PhyloP100

1.7

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over