X-103609426-C-T

Variant names:

• chrX-103609426-C-T
• NM_032926.3:c.362C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032926.3(TCEAL3):​c.362C>T​(p.Ser121Phe) 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 1,098,221 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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: 23)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: TCEAL3 NM_032926.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

Genes affected

TCEAL3 (HGNC:28247): (transcription elongation factor A like 3) 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]

ACMG classification

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=0.15280077).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCEAL3	NM_032926.3	c.362C>T	p.Ser121Phe	missense_variant	Exon 3 of 3	ENST00000372627.10	NP_116315.1
TCEAL3	NM_001006933.2	c.362C>T	p.Ser121Phe	missense_variant	Exon 3 of 3		NP_001006934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCEAL3	ENST00000372627.10	c.362C>T	p.Ser121Phe	missense_variant	Exon 3 of 3	1	NM_032926.3	ENSP00000361710.5
TCEAL3	ENST00000243286.7	c.362C>T	p.Ser121Phe	missense_variant	Exon 3 of 3	1		ENSP00000243286.3
TCEAL3	ENST00000372628.5	c.362C>T	p.Ser121Phe	missense_variant	Exon 3 of 3	5		ENSP00000361711.1
TCEAL3	ENST00000477014.1	n.158+753C>T		intron_variant	Intron 2 of 6	5

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome AF: 9.11e-7 AC: 1 AN: 1098221 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 363585

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	0.18
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.024	T;T;T
FATHMM_MKL	Benign	0.56	D
LIST_S2	Benign	0.81	.;T;.
M_CAP	Benign	0.0028	T
MetaRNN	Benign	0.15	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.3	M;M;M
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-2.0	N;N;N
REVEL	Benign	0.064
Sift	Benign	0.035	D;D;D
Sift4G	Benign	0.080	T;T;T
Polyphen		1.0	D;D;D
Vest4		0.19
MutPred		0.40		Loss of phosphorylation at S121 (P = 0.0016);Loss of phosphorylation at S121 (P = 0.0016);Loss of phosphorylation at S121 (P = 0.0016);
MVP		0.10
MPC		1.3
ClinPred		0.44	T
GERP RS		3.7
Varity_R		0.16
gMVP		0.036

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-102864354; COSMIC: COSV105030971;