NM_001012979.3:c.568G>A

Variant names:

• chrX-103273996-C-T
• NM_001012979.3:c.568G>A

Variant summary

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

The NM_001012979.3(TCEAL5):​c.568G>A​(p.Val190Met) 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: TCEAL5 NM_001012979.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.681
• Publications: 0 publications found

Genes affected

TCEAL5 (HGNC:22282): (transcription elongation factor A like 5) This gene, which is located on the X chromosome, encodes a protein which contains a BEX (brain expressed X-liked like family) domain. This domain is found in proteins encoded by the TCEAL elongation factor (transcription elongation factor A (SII)-like) gene family also located on the X chromosome. The coding region for this gene is located entirely in the terminal exon. [provided by RefSeq, Sep 2011]

ACMG classification

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 (MetaRNN=0.043262154).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012979.3. 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
	TCEAL5	NM_001012979.3	MANE Select	c.568G>A	p.Val190Met	missense	Exon 3 of 3	NP_001012997.1	Q5H9L2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCEAL5	ENST00000372680.2	TSL:1 MANE Select	c.568G>A	p.Val190Met	missense	Exon 3 of 3	ENSP00000361765.1	Q5H9L2
	TCEAL5	ENST00000909247.1		c.568G>A	p.Val190Met	missense	Exon 3 of 3	ENSP00000579306.1
	TCEAL5	ENST00000909248.1		c.568G>A	p.Val190Met	missense	Exon 2 of 2	ENSP00000579307.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

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	0.096
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.27
DANN	Benign	0.13
DEOGEN2	Benign	0.0029	T
FATHMM_MKL	Benign	0.020	N
LIST_S2	Benign	0.70	T
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.043	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		-0.68
PrimateAI	Benign	0.41	T
PROVEAN	Benign	-0.16	N
REVEL	Benign	0.0040
Sift	Benign	0.36	T
Sift4G	Benign	0.25	T
Polyphen		0.0090	B
Vest4		0.22
MutPred		0.23		Loss of sheet (P = 0.0315)
MVP		0.14
MPC		0.64
ClinPred		0.039	T
GERP RS		-1.6
Varity_R		0.045
gMVP		0.017
Mutation Taster		=100/0	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

hg19: chrX-102528924;