Variant 15-82271650-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001348699.2(SAXO2):c.281C>T(p.Pro94Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,612,380 control chromosomes in the GnomAD database, including 194,539 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 15319 hom., cov: 32)

Exomes 𝑓: 0.49 ( 179220 hom. )

Consequence

SAXO2
NM_001348699.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.92

Variant links:

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]

SAXO2 links:

SAXO2 (HGNC:):

SAXO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015205145).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAXO2	NM_001348699.2 linkuse as main transcript	c.281C>T	p.Pro94Leu	missense_variant	3/4	ENST00000682753.1	NP_001335628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SAXO2	ENST00000682753.1 linkuse as main transcript	c.281C>T	p.Pro94Leu	missense_variant	3/4		NM_001348699.2	ENSP00000508095.1	A0A804HKW2
SAXO2	ENST00000339465.5 linkuse as main transcript	c.101C>T	p.Pro34Leu	missense_variant	2/3	1		ENSP00000340445.5	Q658L1-1
SAXO2	ENST00000565501.1 linkuse as main transcript	n.392C>T		non_coding_transcript_exon_variant	2/3	1
SAXO2	ENST00000565432.1 linkuse as main transcript	c.140C>T	p.Pro47Leu	missense_variant	4/4	4		ENSP00000458067.1	H3BVD4

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66649

AN:

151872

Hom.:

15309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.494

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.545

Gnomad NFE

AF:

0.514

Gnomad OTH

AF:

0.459

GnomAD3 exomes

AF:

0.439

AC:

110245

AN:

251040

Hom.:

26228

AF XY:

0.454

AC XY:

61623

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.344

Gnomad AMR exome

AF:

0.235

Gnomad ASJ exome

AF:

0.606

Gnomad EAS exome

AF:

0.211

Gnomad SAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.486

Gnomad NFE exome

AF:

0.510

Gnomad OTH exome

AF:

0.474

GnomAD4 exome

AF:

0.489

AC:

714808

AN:

1460390

Hom.:

179220

Cov.:

AF XY:

0.491

AC XY:

356921

AN XY:

726582

show subpopulations

Gnomad4 AFR exome

AF:

0.340

Gnomad4 AMR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.608

Gnomad4 EAS exome

AF:

0.254

Gnomad4 SAS exome

AF:

0.501

Gnomad4 FIN exome

AF:

0.487

Gnomad4 NFE exome

AF:

0.508

Gnomad4 OTH exome

AF:

0.485

GnomAD4 genome

AF:

0.439

AC:

66680

AN:

151990

Hom.:

15319

Cov.:

AF XY:

0.434

AC XY:

32206

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.351

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.596

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.494

Gnomad4 FIN

AF:

0.472

Gnomad4 NFE

AF:

0.514

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.491

Hom.:

37016

Bravo

AF:

0.419

TwinsUK

AF:

0.512

AC:

1900

ALSPAC

AF:

0.523

AC:

2014

ESP6500AA

AF:

0.360

AC:

1585

ESP6500EA

AF:

0.515

AC:

4433

ExAC

AF:

0.447

AC:

54240

Asia WGS

AF:

0.322

AC:

1122

AN:

3478

EpiCase

AF:

0.513

EpiControl

AF:

0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.071

T;.

Eigen

Uncertain

0.43

Eigen_PC

Uncertain

0.44

FATHMM_MKL

Benign

0.75

LIST_S2

Uncertain

0.89

D;D

MetaRNN

Benign

0.0015

T;T

MetaSVM

Benign

-0.91

MutationTaster

Benign

0.024

P;P;P

PrimateAI

Benign

0.38

PROVEAN

Pathogenic

-5.4

D;D

REVEL

Benign

0.13

Sift

Benign

0.091

T;T

Sift4G

Benign

0.12

T;T

Polyphen

0.87

P;.

Vest4

0.20

MPC

0.38

ClinPred

0.044

GERP RS

3.9

Varity_R

0.083

gMVP

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over