3-172916455-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_031955.6(SPATA16):c.1365G>T(p.Val455=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000788 in 1,613,802 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00082 ( 18 hom. )
Consequence
SPATA16
NM_031955.6 synonymous
NM_031955.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.38
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 -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 3-172916455-C-A is Benign according to our data. Variant chr3-172916455-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 344207.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.38 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA16 | NM_031955.6 | c.1365G>T | p.Val455= | synonymous_variant | 9/11 | ENST00000351008.4 | |
SPATA16 | XM_006713778.4 | c.1365G>T | p.Val455= | synonymous_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA16 | ENST00000351008.4 | c.1365G>T | p.Val455= | synonymous_variant | 9/11 | 1 | NM_031955.6 | P1 | |
SPATA16 | ENST00000652082.1 | c.574G>T | p.Asp192Tyr | missense_variant, NMD_transcript_variant | 6/8 |
Frequencies
GnomAD3 genomes ? AF: 0.000486 AC: 74AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00165 AC: 415AN: 251110Hom.: 6 AF XY: 0.00219 AC XY: 297AN XY: 135700
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GnomAD4 exome AF: 0.000819 AC: 1197AN: 1461540Hom.: 18 Cov.: 33 AF XY: 0.00116 AC XY: 847AN XY: 727106
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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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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