13-111320927-C-G

Variant names:

• chr13-111320927-C-G
• rs201674534
• NM_152324.3:c.37C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_152324.3(TEX29):​c.37C>G​(p.His13Asp) 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H13N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: TEX29 NM_152324.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22125027).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152324.3. 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
	TEX29	NM_152324.3	MANE Select	c.37C>G	p.His13Asp	missense	Exon 2 of 6	NP_689537.1	Q8N6K0
	TEX29	NM_001303133.1		c.-40C>G		5_prime_UTR	Exon 2 of 7	NP_001290062.1	Q8N6K0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX29	ENST00000283547.2	TSL:1 MANE Select	c.37C>G	p.His13Asp	missense	Exon 2 of 6	ENSP00000283547.1	Q8N6K0
	TEX29	ENST00000904792.1		c.37C>G	p.His13Asp	missense	Exon 1 of 5	ENSP00000574851.1
	TEX29	ENST00000497241.5	TSL:5	n.118C>G		non_coding_transcript_exon	Exon 2 of 7	ENSP00000431661.1	F2Z350

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.093	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.72
DEOGEN2	Benign	0.24	T
Eigen	Benign	-0.97
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.071	N
LIST_S2	Benign	0.39	T
M_CAP	Benign	0.0020	T
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.81	L
PhyloP100		1.6
PrimateAI	Uncertain	0.51	T
PROVEAN	Pathogenic	-6.3	D
REVEL	Benign	0.055
Sift	Uncertain	0.016	D
Sift4G	Uncertain	0.028	D
Polyphen		0.23	B
Vest4		0.54
MutPred		0.27		Gain of helix (P = 0.062)
MVP		0.081
MPC		0.41
ClinPred		0.17	T
GERP RS		1.6
PromoterAI		-0.0064	Neutral
Varity_R		0.33
gMVP		0.29
Mutation Taster		=93/7	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: rs201674534; hg19: chr13-111973274;