Genetic Variant SPAG16:c.943-9172G>A (chr2-213480791-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024532.5(SPAG16):c.943-9172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0963 in 152,202 control chromosomes in the GnomAD database, including 1,840 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 0.096 ( 1840 hom., cov: 33)

Consequence

SPAG16
NM_024532.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.385

Publications

0 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:

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new If you want to explore the variant's impact on the transcript NM_024532.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024532.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SPAG16	NM_024532.5	MANE Select	c.943-9172G>A	intron	N/A	NP_078808.3
SPAG16	NR_047659.2		n.1138-9172G>A	intron	N/A
SPAG16	NR_047660.2		n.844-9172G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.943-9172G>A	intron	N/A	ENSP00000332592.5	Q8N0X2-1
SPAG16	ENST00000406979.6	TSL:1	n.*944-9172G>A	intron	N/A	ENSP00000385496.2	F8WB32
SPAG16	ENST00000452556.5	TSL:2	n.*509-9172G>A	intron	N/A	ENSP00000398926.1	F8WBQ0

Frequencies

GnomAD3 genomes

AF:

0.0961

AC:

14617

AN:

152084

Hom.:

1833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0479

Gnomad ASJ

AF:

0.0608

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0381

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0180

Gnomad OTH

AF:

0.0826

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0963

AC:

14657

AN:

152202

Hom.:

1840

Cov.:

AF XY:

0.0931

AC XY:

6927

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.288

AC:

11940

AN:

41498

American (AMR)

AF:

0.0477

AC:

730

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0608

AC:

211

AN:

3472

East Asian (EAS)

AF:

0.00135

AC:

AN:

5190

South Asian (SAS)

AF:

0.0384

AC:

185

AN:

4822

European-Finnish (FIN)

AF:

0.0161

AC:

171

AN:

10608

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0180

AC:

1226

AN:

68000

Other (OTH)

AF:

0.0818

AC:

173

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

571

1143

1714

2286

2857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0615

Hom.:

133

Bravo

AF:

0.108

Asia WGS

AF:

0.0550

AC:

193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

7.0

(source)

DANN

Benign

0.69

PhyloP100

0.39

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over