rs756510648

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_153333.3(TCEAL8):​c.148C>T​(p.Pro50Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,098,261 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 1 hem. )

Consequence

TCEAL8
NM_153333.3 missense

Scores

2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40
Variant links:
Genes affected
TCEAL8 (HGNC:28683): (transcription elongation factor A like 8) 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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07900721).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCEAL8NM_153333.3 linkc.148C>T p.Pro50Ser missense_variant Exon 3 of 3 ENST00000372685.8 NP_699164.1 Q8IYN2
TCEAL8NM_001006684.2 linkc.148C>T p.Pro50Ser missense_variant Exon 2 of 2 NP_001006685.1 Q8IYN2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCEAL8ENST00000372685.8 linkc.148C>T p.Pro50Ser missense_variant Exon 3 of 3 1 NM_153333.3 ENSP00000361770.3 Q8IYN2
TCEAL8ENST00000360000.8 linkc.148C>T p.Pro50Ser missense_variant Exon 2 of 2 1 ENSP00000353093.4 Q8IYN2
TCEAL8ENST00000451678.1 linkc.91-42C>T intron_variant Intron 3 of 3 3 ENSP00000390880.1 Q5H9L1

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
9.11e-7
AC:
1
AN:
1098261
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
1
AN XY:
363615
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.092
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.89
CADD
Benign
14
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0075
T;T
FATHMM_MKL
Benign
0.47
N
LIST_S2
Benign
0.74
.;T
M_CAP
Benign
0.0024
T
MetaRNN
Benign
0.079
T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-0.34
N;N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
0.28
N;N
REVEL
Benign
0.065
Sift
Uncertain
0.017
D;D
Sift4G
Benign
0.46
T;T
Polyphen
0.0090
B;B
Vest4
0.15
MutPred
0.48
Gain of phosphorylation at P50 (P = 0.0124);Gain of phosphorylation at P50 (P = 0.0124);
MVP
0.11
MPC
0.43
ClinPred
0.21
T
GERP RS
4.4
Varity_R
0.094
gMVP
0.43

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-102508760; API