dbSNP rs16850268: SPAG16:c.942+21413A>G (chr2-213396532-A-G) – 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.942+21413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 316,166 control chromosomes in the GnomAD database, including 2,242 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 0.099 ( 1947 hom., cov: 32)

Exomes 𝑓: 0.033 ( 295 hom. )

Consequence

SPAG16
NM_024532.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.165

Publications

1 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5 link	c.942+21413A>G		intron_variant	Intron 9 of 15	ENST00000331683.10	NP_078808.3	Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SPAG16	ENST00000331683.10 link	c.942+21413A>G	intron_variant	Intron 9 of 15	1	NM_024532.5	ENSP00000332592.5	Q8N0X2-1
SPAG16	ENST00000447990.1 link	c.942+21413A>G	intron_variant	Intron 9 of 9	1		ENSP00000400847.1	E7EWV3
SPAG16	ENST00000406979.6 link	n.*943+21413A>G	intron_variant	Intron 11 of 17	1		ENSP00000385496.2	F8WB32
SPAG16	ENST00000452556.5 link	n.*508+21413A>G	intron_variant	Intron 7 of 13	2		ENSP00000398926.1	F8WBQ0

Frequencies

GnomAD3 genomes

AF:

0.0987

AC:

15020

AN:

152112

Hom.:

1937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.297

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0487

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.0160

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0180

Gnomad OTH

AF:

0.0819

GnomAD4 exome

AF:

0.0330

AC:

5404

AN:

163938

Hom.:

295

AF XY:

0.0329

AC XY:

3064

AN XY:

93052

show subpopulations

African (AFR)

AF:

0.306

AC:

1317

AN:

4306

American (AMR)

AF:

0.0269

AC:

325

AN:

12098

Ashkenazi Jewish (ASJ)

AF:

0.0659

AC:

352

AN:

5338

East Asian (EAS)

AF:

0.00120

AC:

AN:

5846

South Asian (SAS)

AF:

0.0412

AC:

1343

AN:

32574

European-Finnish (FIN)

AF:

0.0144

AC:

121

AN:

8426

Middle Eastern (MID)

AF:

0.0517

AC:

116

AN:

2242

European-Non Finnish (NFE)

AF:

0.0176

AC:

1497

AN:

85128

Other (OTH)

AF:

0.0409

AC:

326

AN:

7980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

219

438

658

877

1096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.0990

AC:

15064

AN:

152228

Hom.:

1947

Cov.:

AF XY:

0.0956

AC XY:

7116

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.297

AC:

12344

AN:

41508

American (AMR)

AF:

0.0485

AC:

742

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

211

AN:

3470

East Asian (EAS)

AF:

0.00135

AC:

AN:

5184

South Asian (SAS)

AF:

0.0373

AC:

180

AN:

4820

European-Finnish (FIN)

AF:

0.0160

AC:

170

AN:

10620

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0180

AC:

1225

AN:

68022

Other (OTH)

AF:

0.0810

AC:

171

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

573

1146

1719

2292

2865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.157

Hom.:

771

Bravo

AF:

0.111

Asia WGS

AF:

0.0570

AC:

200

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.3

(source)

DANN

Benign

0.78

PhyloP100

0.17

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