10-22386815-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012443.4(SPAG6):c.534G>A(p.Glu178=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000347 in 1,613,602 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 5 hom. )
Consequence
SPAG6
NM_012443.4 synonymous
NM_012443.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 6.72
Genes affected
SPAG6 (HGNC:11215): (sperm associated antigen 6) The correlation of anti-sperm antibodies with cases of unexplained infertility implicates a role for these antibodies in blocking fertilization. Improved diagnosis and treatment of immunologic infertility, as well as identification of proteins for targeted contraception, are dependent on the identification and characterization of relevant sperm antigens. The protein expressed by this gene is recognized by anti-sperm antibodies from an infertile man. This protein localizes to the tail of permeabilized human sperm and contains eight contiguous armadillo repeats, a motif known to mediate protein-protein interactions. Studies in mice suggest that this protein is involved in sperm flagellar motility and maintenance of the structural integrity of mature sperm. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 10-22386815-G-A is Benign according to our data. Variant chr10-22386815-G-A is described in ClinVar as [Benign]. Clinvar id is 718025.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPAG6 | NM_012443.4 | c.534G>A | p.Glu178= | synonymous_variant | 5/11 | ENST00000376624.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPAG6 | ENST00000376624.8 | c.534G>A | p.Glu178= | synonymous_variant | 5/11 | 1 | NM_012443.4 | P1 | |
ENST00000422675.1 | n.250+25394G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152128Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000733 AC: 184AN: 250996Hom.: 1 AF XY: 0.000988 AC XY: 134AN XY: 135644
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GnomAD4 exome AF: 0.000361 AC: 527AN: 1461356Hom.: 5 Cov.: 31 AF XY: 0.000517 AC XY: 376AN XY: 726994
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GnomAD4 genome AF: 0.000217 AC: 33AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 01, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at