rs16973457

Variant names:

• chr15-82271650-C-A
• rs16973457
• NM_001348699.2:c.281C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Uncertain significance. The variant received 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. 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SAXO2 NM_001348699.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92
• Publications: 40 publications found

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

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=0.17296267).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348699.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO2	NM_001348699.2	MANE Select	c.281C>A	p.Pro94Gln	missense	Exon 3 of 4	NP_001335628.1
	SAXO2	NM_001348700.2		c.140C>A	p.Pro47Gln	missense	Exon 3 of 4	NP_001335629.1
	SAXO2	NM_001348701.2		c.140C>A	p.Pro47Gln	missense	Exon 4 of 5	NP_001335630.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAXO2	ENST00000682753.1	MANE Select	c.281C>A	p.Pro94Gln	missense	Exon 3 of 4	ENSP00000508095.1
	SAXO2	ENST00000339465.5	TSL:1	c.101C>A	p.Pro34Gln	missense	Exon 2 of 3	ENSP00000340445.5
	SAXO2	ENST00000565501.1	TSL:1	n.392C>A		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 42

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 49168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-1.1	T
PhyloP100		2.9
PrimateAI	Benign	0.35	T
PROVEAN	Uncertain	-3.5	D
REVEL	Benign	0.049
Sift	Benign	0.33	T
Sift4G	Benign	0.64	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

Other links and lift over

dbSNP: rs16973457; hg19: chr15-82563991;