2-213683813-G-A

Variant summary

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

The NM_024532.5(SPAG16):​c.1071-178672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,020 control chromosomes in the GnomAD database, including 4,146 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 0.21 ( 4146 hom., cov: 32)

Consequence

SPAG16
NM_024532.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

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]

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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPAG16NM_024532.5 linkc.1071-178672G>A intron_variant Intron 10 of 15 ENST00000331683.10 NP_078808.3 Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPAG16ENST00000331683.10 linkc.1071-178672G>A intron_variant Intron 10 of 15 1 NM_024532.5 ENSP00000332592.5 Q8N0X2-1
SPAG16ENST00000406979.6 linkn.*1072-178672G>A intron_variant Intron 12 of 17 1 ENSP00000385496.2 F8WB32
SPAG16ENST00000451561.1 linkc.129-178672G>A intron_variant Intron 1 of 5 3 ENSP00000416600.1 H0Y811
SPAG16ENST00000452556.5 linkn.*637-178672G>A intron_variant Intron 8 of 13 2 ENSP00000398926.1 F8WBQ0

Frequencies

GnomAD3 genomes
AF:
0.209
AC:
31794
AN:
151902
Hom.:
4147
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0618
Gnomad AMI
AF:
0.157
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.320
Gnomad EAS
AF:
0.355
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.218
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.275
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.209
AC:
31789
AN:
152020
Hom.:
4146
Cov.:
32
AF XY:
0.208
AC XY:
15417
AN XY:
74296
show subpopulations
African (AFR)
AF:
0.0616
AC:
2556
AN:
41502
American (AMR)
AF:
0.224
AC:
3417
AN:
15256
Ashkenazi Jewish (ASJ)
AF:
0.320
AC:
1108
AN:
3466
East Asian (EAS)
AF:
0.355
AC:
1833
AN:
5158
South Asian (SAS)
AF:
0.227
AC:
1092
AN:
4818
European-Finnish (FIN)
AF:
0.218
AC:
2297
AN:
10538
Middle Eastern (MID)
AF:
0.320
AC:
94
AN:
294
European-Non Finnish (NFE)
AF:
0.276
AC:
18727
AN:
67968
Other (OTH)
AF:
0.248
AC:
522
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1226
2452
3677
4903
6129
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
344
688
1032
1376
1720
<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:
0.198
Hom.:
2660
Bravo
AF:
0.206
Asia WGS
AF:
0.218
AC:
754
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.062
DANN
Benign
0.37
PhyloP100
-1.3
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs6707387; hg19: chr2-214548537; API