rs16973457

Positions:

• chr15-82271650-C-A
• chr15-82271650-C-T

Variant summary

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

The NM_001348699.2(SAXO2):​c.281C>A​(p.Pro94Gln) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SAXO2 NM_001348699.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92

Genes affected

SAXO2 (HGNC:33727): (stabilizer of axonemal microtubules 2) Predicted to enable microtubule binding activity. Predicted to be involved in microtubule anchoring. Predicted to be active in microtubule cytoskeleton; nucleus; and sperm flagellum. [provided by Alliance of Genome Resources, Apr 2022]

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=0.17296267).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAXO2	NM_001348699.2	c.281C>A	p.Pro94Gln	missense_variant	3/4	ENST00000682753.1	NP_001335628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAXO2	ENST00000682753.1	c.281C>A	p.Pro94Gln	missense_variant	3/4		NM_001348699.2	ENSP00000508095	A2
SAXO2	ENST00000339465.5	c.101C>A	p.Pro34Gln	missense_variant	2/3	1		ENSP00000340445	P2
SAXO2	ENST00000565501.1	n.392C>A		non_coding_transcript_exon_variant	2/3	1
SAXO2	ENST00000565432.1	c.140C>A	p.Pro47Gln	missense_variant	4/4	4		ENSP00000458067	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 42

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.80
DEOGEN2	Benign	0.025	T;.
Eigen	Benign	-0.084
Eigen_PC	Benign	0.073
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.73	T;T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.17	T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	0.92	P;P;P
PrimateAI	Benign	0.35	T
PROVEAN	Uncertain	-3.5	D;D
REVEL	Benign	0.049
Sift	Benign	0.33	T;T
Sift4G	Benign	0.64	T;T
Polyphen		0.097	B;.
Vest4		0.14
MutPred		0.28		Loss of ubiquitination at K38 (P = 0.0877);.;
MVP		0.16
MPC		0.21
ClinPred		0.81	D
GERP RS		3.9
Varity_R		0.11
gMVP		0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs16973457; hg19: chr15-82563991;