2-213340200-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024532.5(SPAG16):c.574C>T(p.Arg192Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000138 in 1,611,238 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
SPAG16
NM_024532.5 missense
NM_024532.5 missense
Scores
1
11
6
Clinical Significance
Conservation
PhyloP100: 3.61
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.03172636).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPAG16 | NM_024532.5 | c.574C>T | p.Arg192Cys | missense_variant | 6/16 | ENST00000331683.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPAG16 | ENST00000331683.10 | c.574C>T | p.Arg192Cys | missense_variant | 6/16 | 1 | NM_024532.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 151692Hom.: 0 Cov.: 32
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?
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GnomAD3 exomes AF: 0.000233 AC: 58AN: 248522Hom.: 0 AF XY: 0.000268 AC XY: 36AN XY: 134430
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GnomAD4 exome AF: 0.000136 AC: 198AN: 1459428Hom.: 1 Cov.: 30 AF XY: 0.000163 AC XY: 118AN XY: 725922
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GnomAD4 genome ? AF: 0.000158 AC: 24AN: 151810Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74168
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.574C>T (p.R192C) alteration is located in exon 6 (coding exon 6) of the SPAG16 gene. This alteration results from a C to T substitution at nucleotide position 574, causing the arginine (R) at amino acid position 192 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;D;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
0.63
.;P;.;.
Vest4
0.67, 0.73, 0.75
MVP
MPC
0.18
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at