Genetic Variant NM_152278.5:c.-94G>A (chrX-103330974-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is . The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_152278.5(TCEAL7):c.-94G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

TCEAL7
NM_152278.5 5_prime_UTR

Scores

Splicing: ADA: 0.0002553

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:

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new If you want to explore the variant's impact on the transcript NM_152278.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152278.5. 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>A		5_prime_UTR	Exon 2 of 3	NP_689491.1	Q9BRU2
	TCEAL7	NM_001348258.2		c.-91-3G>A		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>A	5_prime_UTR	Exon 2 of 3	ENSP00000329794.4	Q9BRU2
TCEAL7	ENST00000861133.1		c.-94G>A	5_prime_UTR	Exon 1 of 2	ENSP00000531192.1
TCEAL7	ENST00000932017.1		c.-92G>A	5_prime_UTR	Exon 2 of 3	ENSP00000602076.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

3599

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

833

African (AFR)

AF:

0.00

AC:

AN:

103

American (AMR)

AF:

0.00

AC:

AN:

262

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

113

South Asian (SAS)

AF:

0.00

AC:

AN:

101

European-Finnish (FIN)

AF:

0.00

AC:

AN:

377

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

2370

Other (OTH)

AF:

0.00

AC:

AN:

179

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00026

dbscSNV1_RF

Benign

0.038

SpliceAI score (max)

0.23

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.23

Position offset: 3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over