Variant rs61752199 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_024532.5(SPAG16):c.1067G>A(p.Ser356Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 1,573,270 control chromosomes in the GnomAD database, including 335 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 24 hom., cov: 32)

Exomes 𝑓: 0.017 ( 311 hom. )

Consequence

SPAG16
NM_024532.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.56

Variant links:

Genes affected

SPAG16 (HGNC:23225): (sperm associated antigen 16) Cilia and flagella are comprised of a microtubular backbone, the axoneme, which is organized by the basal body and surrounded by plasma membrane. SPAG16 encodes 2 major proteins that associate with the axoneme of sperm tail and the nucleus of postmeiotic germ cells, respectively (Zhang et al., 2007 [PubMed 17699735]).[supplied by OMIM, Jul 2008]

SPAG16 links:

SPAG16 (HGNC:):

SPAG16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0043849945).

BP6

Variant 2-213490087-G-A is Benign according to our data. Variant chr2-213490087-G-A is described in ClinVar as [Benign]. Clinvar id is 3341511.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0146 (2215/152224) while in subpopulation SAS AF= 0.0381 (184/4826). AF 95% confidence interval is 0.0336. There are 24 homozygotes in gnomad4. There are 1086 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 24 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPAG16	NM_024532.5 linkuse as main transcript	c.1067G>A	p.Ser356Asn	missense_variant	10/16	ENST00000331683.10	NP_078808.3	Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10 linkuse as main transcript	c.1067G>A	p.Ser356Asn	missense_variant	10/16	1	NM_024532.5	ENSP00000332592.5		Q8N0X2-1

Frequencies

GnomAD3 genomes

AF:

0.0145

AC:

2210

AN:

152106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00777

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0377

Gnomad FIN

AF:

0.0131

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0161

Gnomad OTH

AF:

0.0158

GnomAD3 exomes

AF:

0.0179

AC:

3892

AN:

217896

Hom.:

AF XY:

0.0194

AC XY:

2302

AN XY:

118516

show subpopulations

Gnomad AFR exome

AF:

0.00678

Gnomad AMR exome

AF:

0.00898

Gnomad ASJ exome

AF:

0.0628

Gnomad EAS exome

AF:

0.00199

Gnomad SAS exome

AF:

0.0425

Gnomad FIN exome

AF:

0.0103

Gnomad NFE exome

AF:

0.0157

Gnomad OTH exome

AF:

0.0233

GnomAD4 exome

AF:

0.0170

AC:

24173

AN:

1421046

Hom.:

311

Cov.:

AF XY:

0.0178

AC XY:

12584

AN XY:

706484

show subpopulations

Gnomad4 AFR exome

AF:

0.00834

Gnomad4 AMR exome

AF:

0.00903

Gnomad4 ASJ exome

AF:

0.0618

Gnomad4 EAS exome

AF:

0.00132

Gnomad4 SAS exome

AF:

0.0417

Gnomad4 FIN exome

AF:

0.0118

Gnomad4 NFE exome

AF:

0.0153

Gnomad4 OTH exome

AF:

0.0197

GnomAD4 genome

AF:

0.0146

AC:

2215

AN:

152224

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1086

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00782

Gnomad4 AMR

AF:

0.0142

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0381

Gnomad4 FIN

AF:

0.0131

Gnomad4 NFE

AF:

0.0161

Gnomad4 OTH

AF:

0.0157

Alfa

AF:

0.0164

Hom.:

Bravo

AF:

0.0132

TwinsUK

AF:

0.0175

AC:

ALSPAC

AF:

0.0143

AC:

ESP6500AA

AF:

0.00750

AC:

ESP6500EA

AF:

0.0179

AC:

154

ExAC

AF:

0.0184

AC:

2228

Asia WGS

AF:

0.0350

AC:

121

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2024

SPAG16: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.48

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.37

T;.

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.39

FATHMM_MKL

Benign

0.69

LIST_S2

Benign

0.50

T;T

MetaRNN

Benign

0.0044

T;T

MetaSVM

Benign

-0.41

MutationAssessor

Benign

1.8

L;.

PrimateAI

Uncertain

0.51

PROVEAN

Uncertain

-2.7

D;N

REVEL

Benign

0.22

Sift

Uncertain

0.0020

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

0.87

P;.

Vest4

0.081

MPC

0.15

ClinPred

0.014

GERP RS

5.0

Varity_R

0.60

gMVP

0.25

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over