15-56391344-G-A

Position:

• chr15-56391344-G-A

Variant summary

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

The NM_001395496.1(TEX9):​c.497G>A​(p.Gly166Glu) 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. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TEX9 NM_001395496.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.67

Genes affected

TEX9 (HGNC:29585): (testis expressed 9)

TEX9 (HGNC:):

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=0.122080356).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX9	NM_001395496.1	c.497G>A	p.Gly166Glu	missense_variant	7/12	ENST00000696102.1	NP_001382425.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TEX9	ENST00000696102.1	c.497G>A	p.Gly166Glu	missense_variant	7/12		NM_001395496.1	ENSP00000512397.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 01, 2022

The c.497G>A (p.G166E) alteration is located in exon 7 (coding exon 7) of the TEX9 gene. This alteration results from a G to A substitution at nucleotide position 497, causing the glycine (G) at amino acid position 166 to be replaced by a glutamic acid (E). 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	0.12
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Uncertain	1.0
DEOGEN2	Benign	0.20	.;T;.;.;.
Eigen	Benign	-0.041
Eigen_PC	Benign	0.074
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.73	T;T;T;T;T
M_CAP	Benign	0.0024	T
MetaRNN	Benign	0.12	T;T;T;T;T
MetaSVM	Benign	-0.86	T
MutationAssessor	Uncertain	2.1	.;M;.;.;.
PrimateAI	Benign	0.41	T
PROVEAN	Pathogenic	-5.9	D;N;D;N;D
REVEL	Benign	0.13
Sift	Benign	0.13	T;T;T;T;T
Sift4G	Benign	0.090	T;T;T;T;D
Polyphen		0.60	.;P;.;.;.
Vest4		0.17, 0.17, 0.24, 0.28
MutPred		0.17		.;Gain of disorder (P = 0.0621);.;Gain of disorder (P = 0.0621);.;
MVP		0.12
MPC		0.018
ClinPred		0.96	D
GERP RS		4.9
Varity_R		0.31
gMVP		0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr15-56683542;