13-111339902-C-G

Variant names:

• chr13-111339902-C-G
• NM_152324.3:c.209C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_152324.3(TEX29):​c.209C>G​(p.Ala70Gly) 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A70T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TEX29 NM_152324.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.802

Genes affected

TEX29 (HGNC:20370): (testis expressed 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.3049278).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX29	NM_152324.3	c.209C>G	p.Ala70Gly	missense_variant	Exon 4 of 6	ENST00000283547.2	NP_689537.1
TEX29	NM_001303133.1	c.278C>G	p.Ala93Gly	missense_variant	Exon 5 of 7		NP_001290062.1
TEX29	XM_017020387.2	c.290C>G	p.Ala97Gly	missense_variant	Exon 4 of 6		XP_016875876.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX29	ENST00000283547.2	c.209C>G	p.Ala70Gly	missense_variant	Exon 4 of 6	1	NM_152324.3	ENSP00000283547.1
TEX29	ENST00000497241.5	n.*180C>G		non_coding_transcript_exon_variant	Exon 5 of 7	5		ENSP00000431661.1
TEX29	ENST00000497241.5	n.*180C>G		3_prime_UTR_variant	Exon 5 of 7	5		ENSP00000431661.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Nov 06, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.209C>G (p.A70G) alteration is located in exon 4 (coding exon 3) of the TEX29 gene. This alteration results from a C to G substitution at nucleotide position 209, causing the alanine (A) at amino acid position 70 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.24	T
Eigen	Benign	-0.24
Eigen_PC	Benign	-0.39
FATHMM_MKL	Benign	0.046	N
LIST_S2	Benign	0.50	T
M_CAP	Benign	0.0030	T
MetaRNN	Benign	0.30	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.97	L
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-3.4	D
REVEL	Benign	0.052
Sift	Benign	0.057	T
Sift4G	Uncertain	0.033	D
Polyphen		0.96	D
Vest4		0.39
MutPred		0.27		Gain of sheet (P = 0.0344);
MVP		0.14
MPC		0.66
ClinPred		0.59	D
GERP RS		3.2
Varity_R		0.16
gMVP		0.095

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr13-111992249;