Genetic Variant TCEAL7:c.-94G>C (chrX-103330974-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152278.5(TCEAL7):c.-94G>C variant causes a 5 prime UTR 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 0.62 ( 16585 hom., 19699 hem., cov: 22)

Exomes 𝑓: 0.51 ( 396 hom. 421 hem. )

Failed GnomAD Quality Control

Consequence

TCEAL7
NM_152278.5 5_prime_UTR

Scores

Splicing: ADA: 0.00004452

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.363

Publications

7 publications found

Variant links:

Genes affected

TCEAL7 (HGNC:28336): (transcription elongation factor A like 7) Predicted to enable WW domain binding activity. Involved in negative regulation of NF-kappaB transcription factor activity and negative regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TCEAL7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEAL7	NM_152278.5 link	c.-94G>C		5_prime_UTR_variant	Exon 2 of 3	ENST00000332431.5	NP_689491.1
TCEAL7	NM_001348258.2 link	c.-91-3G>C		splice_region_variant, intron_variant	Intron 1 of 2		NP_001335187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEAL7	ENST00000332431.5 link	c.-94G>C		5_prime_UTR_variant	Exon 2 of 3	1	NM_152278.5	ENSP00000329794.4		Q9BRU2
TCEAL7	ENST00000372666.1 link	c.-91-3G>C		splice_region_variant, intron_variant	Intron 1 of 2	2		ENSP00000361751.1		Q9BRU2

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

68240

AN:

109842

Hom.:

16581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.899

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.632

Gnomad EAS

AF:

0.590

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.422

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.611

GnomAD4 exome

AF:

0.505

AC:

1810

AN:

3582

Hom.:

396

Cov.:

AF XY:

0.508

AC XY:

421

AN XY:

828

show subpopulations

African (AFR)

AF:

0.922

AC:

AN:

103

American (AMR)

AF:

0.595

AC:

156

AN:

262

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

AN:

East Asian (EAS)

AF:

0.541

AC:

AN:

111

South Asian (SAS)

AF:

0.782

AC:

AN:

101

European-Finnish (FIN)

AF:

0.446

AC:

168

AN:

377

Middle Eastern (MID)

AF:

0.400

AC:

AN:

European-Non Finnish (NFE)

AF:

0.469

AC:

1104

AN:

2356

Other (OTH)

AF:

0.494

AC:

AN:

178

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

125

156

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

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.621

AC:

68297

AN:

109894

Hom.:

16585

Cov.:

AF XY:

0.612

AC XY:

19699

AN XY:

32188

show subpopulations

African (AFR)

AF:

0.899

AC:

27031

AN:

30064

American (AMR)

AF:

0.591

AC:

6135

AN:

10377

Ashkenazi Jewish (ASJ)

AF:

0.632

AC:

1657

AN:

2620

East Asian (EAS)

AF:

0.590

AC:

2040

AN:

3457

South Asian (SAS)

AF:

0.742

AC:

1862

AN:

2508

European-Finnish (FIN)

AF:

0.422

AC:

2464

AN:

5833

Middle Eastern (MID)

AF:

0.521

AC:

113

AN:

217

European-Non Finnish (NFE)

AF:

0.492

AC:

25925

AN:

52654

Other (OTH)

AF:

0.611

AC:

911

AN:

1490

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

795

1589

2384

3178

3973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.557

Hom.:

4269

Bravo

AF:

0.647

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

(source)

DANN

Benign

0.55

PhyloP100

0.36

Mutation Taster

=82/18

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000045

dbscSNV1_RF

Benign

0.0080

SpliceAI score (max)

0.25

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.25

Position offset: 3

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