X-102126844-T-G

Variant names:

• chrX-102126844-T-G
• rs201161155
• NM_080390.4:c.14T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_080390.4(TCEAL2):​c.14T>G​(p.Phe5Cys) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F5Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 24)
• Consequence: TCEAL2 NM_080390.4 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.550
• Publications: 0 publications found

Genes affected

TCEAL2 (HGNC:29818): (transcription elongation factor A like 2) 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. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.046472937).
• BP6: Variant X-102126844-T-G is Benign according to our data. Variant chrX-102126844-T-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3966384.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080390.4. 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
	TCEAL2	NM_080390.4	MANE Select	c.14T>G	p.Phe5Cys	missense	Exon 3 of 3	NP_525129.1	Q9H3H9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEAL2	ENST00000372780.6	TSL:1 MANE Select	c.14T>G	p.Phe5Cys	missense	Exon 3 of 3	ENSP00000361866.1	Q9H3H9
	TCEAL2	ENST00000476749.1	TSL:1	n.799T>G		non_coding_transcript_exon	Exon 2 of 2
	TCEAL2	ENST00000329035.2	TSL:5	c.14T>G	p.Phe5Cys	missense	Exon 3 of 3	ENSP00000332359.2	Q9H3H9

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.047
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.30
DEOGEN2	Benign	0.0023	T
FATHMM_MKL	Benign	0.00035	N
LIST_S2	Benign	0.19	T
M_CAP	Benign	0.00084	T
MetaRNN	Benign	0.046	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	-1.2	N
PhyloP100		-0.55
PrimateAI	Benign	0.39	T
PROVEAN	Benign	0.60	N
REVEL	Benign	0.012
Sift	Benign	0.29	T
Sift4G	Benign	0.19	T
Polyphen		0.0	B
Vest4		0.074
MutPred		0.27		Loss of sheet (P = 0.1907)
MVP		0.043
MPC		0.45
ClinPred		0.20	T
GERP RS		-6.8
Varity_R		0.051
gMVP		0.012
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs201161155; hg19: chrX-101381816;