dbSNP rs16851495: SPAG16:c.1593+26G>A (chr2-214108287-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024532.5(SPAG16):c.1593+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,551,664 control chromosomes in the GnomAD database, including 5,883 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 0.088 ( 765 hom., cov: 32)

Exomes 𝑓: 0.074 ( 5118 hom. )

Consequence

SPAG16
NM_024532.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.52

Publications

6 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5 link	c.1593+26G>A		intron_variant	Intron 14 of 15	ENST00000331683.10	NP_078808.3	Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10 link	c.1593+26G>A		intron_variant	Intron 14 of 15	1	NM_024532.5	ENSP00000332592.5		Q8N0X2-1

Frequencies

GnomAD3 genomes

AF:

0.0876

AC:

13306

AN:

151906

Hom.:

764

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.0706

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.0884

Gnomad FIN

AF:

0.0655

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0644

Gnomad OTH

AF:

0.0934

GnomAD2 exomes

AF:

0.0892

AC:

21361

AN:

239522

AF XY:

0.0870

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.0729

Gnomad ASJ exome

AF:

0.0875

Gnomad EAS exome

AF:

0.277

Gnomad FIN exome

AF:

0.0784

Gnomad NFE exome

AF:

0.0653

Gnomad OTH exome

AF:

0.0855

GnomAD4 exome

AF:

0.0742

AC:

103870

AN:

1399640

Hom.:

5118

Cov.:

AF XY:

0.0743

AC XY:

51676

AN XY:

695934

show subpopulations

African (AFR)

AF:

0.116

AC:

3701

AN:

31822

American (AMR)

AF:

0.0730

AC:

3027

AN:

41490

Ashkenazi Jewish (ASJ)

AF:

0.0854

AC:

2138

AN:

25044

East Asian (EAS)

AF:

0.300

AC:

11709

AN:

39076

South Asian (SAS)

AF:

0.0790

AC:

6472

AN:

81954

European-Finnish (FIN)

AF:

0.0756

AC:

3998

AN:

52854

Middle Eastern (MID)

AF:

0.0953

AC:

534

AN:

5606

European-Non Finnish (NFE)

AF:

0.0632

AC:

67202

AN:

1063680

Other (OTH)

AF:

0.0876

AC:

5089

AN:

58114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

4287

8573

12860

17146

21433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2734

5468

8202

10936

13670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0876

AC:

13316

AN:

152024

Hom.:

765

Cov.:

AF XY:

0.0884

AC XY:

6566

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.115

AC:

4753

AN:

41488

American (AMR)

AF:

0.0705

AC:

1075

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0784

AC:

272

AN:

3470

East Asian (EAS)

AF:

0.286

AC:

1475

AN:

5166

South Asian (SAS)

AF:

0.0879

AC:

423

AN:

4814

European-Finnish (FIN)

AF:

0.0655

AC:

692

AN:

10564

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0644

AC:

4379

AN:

67960

Other (OTH)

AF:

0.0934

AC:

197

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

616

1232

1849

2465

3081

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

154

308

462

616

770

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0732

Hom.:

111

Bravo

AF:

0.0918

Asia WGS

AF:

0.181

AC:

628

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.018

(source)

DANN

Benign

0.59

PhyloP100

-3.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over