rs10498008

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.385
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]

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 (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPAG16NM_024532.5 linkuse as main transcriptc.943-9172G>A intron_variant ENST00000331683.10 NP_078808.3 Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPAG16ENST00000331683.10 linkuse as main transcriptc.943-9172G>A intron_variant 1 NM_024532.5 ENSP00000332592.5 Q8N0X2-1
SPAG16ENST00000406979.6 linkuse as main transcriptn.*944-9172G>A intron_variant 1 ENSP00000385496.2 F8WB32
SPAG16ENST00000452556.5 linkuse as main transcriptn.*509-9172G>A intron_variant 2 ENSP00000398926.1 F8WBQ0

Frequencies

GnomAD3 genomes
AF:
0.0961
AC:
14617
AN:
152084
Hom.:
1833
Cov.:
33
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.:
33
AF XY:
0.0931
AC XY:
6927
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.288
Gnomad4 AMR
AF:
0.0477
Gnomad4 ASJ
AF:
0.0608
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0384
Gnomad4 FIN
AF:
0.0161
Gnomad4 NFE
AF:
0.0180
Gnomad4 OTH
AF:
0.0818
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.0
DANN
Benign
0.69

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.

Other links and lift over

dbSNP: rs10498008; hg19: chr2-214345515; API