chr3-172913722-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_031955.6(SPATA16):c.1526C>T(p.Ala509Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 1,613,078 control chromosomes in the GnomAD database, including 455 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.019 ( 29 hom., cov: 32)
Exomes 𝑓: 0.022 ( 426 hom. )
Consequence
SPATA16
NM_031955.6 missense
NM_031955.6 missense
Scores
2
6
10
Clinical Significance
Conservation
PhyloP100: 7.52
Genes affected
SPATA16 (HGNC:29935): (spermatogenesis associated 16) This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008070976).
BP6
?
Variant 3-172913722-G-A is Benign according to our data. Variant chr3-172913722-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 344204.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0188 (2857/152178) while in subpopulation NFE AF= 0.0245 (1667/68008). AF 95% confidence interval is 0.0235. There are 29 homozygotes in gnomad4. There are 1406 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 29 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA16 | NM_031955.6 | c.1526C>T | p.Ala509Val | missense_variant | 10/11 | ENST00000351008.4 | |
SPATA16 | XM_006713778.4 | c.1526C>T | p.Ala509Val | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA16 | ENST00000351008.4 | c.1526C>T | p.Ala509Val | missense_variant | 10/11 | 1 | NM_031955.6 | P1 | |
SPATA16 | ENST00000652082.1 | c.*90C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0188 AC: 2855AN: 152060Hom.: 29 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0190 AC: 4776AN: 251004Hom.: 66 AF XY: 0.0193 AC XY: 2613AN XY: 135656
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GnomAD4 exome AF: 0.0217 AC: 31739AN: 1460900Hom.: 426 Cov.: 30 AF XY: 0.0216 AC XY: 15681AN XY: 726752
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ESP6500AA
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Globozoospermia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MPC
ClinPred
T
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