NM_032126.5:c.289G>A

Variant names:

• chr1-178520384-G-A
• rs139746729
• NM_032126.5:c.289G>A

Variant summary

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

The NM_032126.5(TEX35):​c.289G>A​(p.Asp97Asn) 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. 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. D97Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TEX35 NM_032126.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.79
• Publications: 1 publications found

Genes affected

TEX35 (HGNC:25366): (testis expressed 35) Located in microtubule cytoskeleton. [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=0.23970479).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEX35	NM_032126.5	c.289G>A	p.Asp97Asn	missense_variant	Exon 6 of 9	ENST00000319416.7	NP_115502.2
TEX35	NM_001170722.2	c.313G>A	p.Asp105Asn	missense_variant	Exon 6 of 9		NP_001164193.1
TEX35	NM_001170723.2	c.289G>A	p.Asp97Asn	missense_variant	Exon 6 of 9		NP_001164194.1
TEX35	NM_001170724.2	c.289G>A	p.Asp97Asn	missense_variant	Exon 6 of 9		NP_001164195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEX35	ENST00000319416.7	c.289G>A	p.Asp97Asn	missense_variant	Exon 6 of 9	1	NM_032126.5	ENSP00000323795.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Pathogenic	26
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.038	T;.;.;.
Eigen	Uncertain	0.44
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Uncertain	0.88	D;D;D;D
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.24	T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	1.0	L;L;L;.
PhyloP100		2.8
PrimateAI	Uncertain	0.64	T
PROVEAN	Uncertain	-4.2	D;D;D;D
REVEL	Benign	0.14
Sift	Benign	0.052	T;T;T;T
Sift4G	Benign	0.088	T;T;T;T
Polyphen		0.99	D;.;D;P
Vest4		0.35
MutPred		0.35		Gain of MoRF binding (P = 0.0678);Gain of MoRF binding (P = 0.0678);Gain of MoRF binding (P = 0.0678);.;
MVP		0.30
MPC		0.44
ClinPred		0.99	D
GERP RS		3.7
PromoterAI		0.024	Neutral
Varity_R		0.21
gMVP		0.27
Mutation Taster		=94/6	polymorphism

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

Other links and lift over

dbSNP: rs139746729; hg19: chr1-178489519;