dbSNP rs1045761: 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_001348258.2(TCEAL7):c.-91-3G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as (no stars).

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_001348258.2 splice_region, intron

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348258.2. 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
	TCEAL7	NM_152278.5	MANE Select	c.-94G>C		5_prime_UTR	Exon 2 of 3	NP_689491.1	Q9BRU2
	TCEAL7	NM_001348258.2		c.-91-3G>C		splice_region intron	N/A	NP_001335187.1	Q9BRU2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TCEAL7	ENST00000332431.5	TSL:1 MANE Select	c.-94G>C	5_prime_UTR	Exon 2 of 3	ENSP00000329794.4	Q9BRU2
TCEAL7	ENST00000861133.1		c.-94G>C	5_prime_UTR	Exon 1 of 2	ENSP00000531192.1
TCEAL7	ENST00000932017.1		c.-92G>C	5_prime_UTR	Exon 2 of 3	ENSP00000602076.1

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 v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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