chr8-100161958-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003114.5(SPAG1):c.-2-321A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,076 control chromosomes in the GnomAD database, including 28,951 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 28951 hom., cov: 32)
Consequence
SPAG1
NM_003114.5 intron
NM_003114.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.80
Genes affected
SPAG1 (HGNC:11212): (sperm associated antigen 1) 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 agglutinating antibodies from an infertile woman. Furthermore, immunization of female rats with the recombinant human protein reduced fertility. This protein localizes to the plasma membrane of germ cells in the testis and to the post-acrosomal plasma membrane of mature spermatozoa. Recombinant polypeptide binds GTP and exhibits GTPase activity. Thus, this protein may regulate GTP signal transduction pathways involved in spermatogenesis and fertilization. Two transcript variants of this gene encode the same protein. [provided by RefSeq, Jul 2008]
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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 (BayesDel_noAF=-1.02).
BP6
Variant 8-100161958-A-C is Benign according to our data. Variant chr8-100161958-A-C is described in ClinVar as [Benign]. Clinvar id is 1241493.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPAG1 | NM_003114.5 | c.-2-321A>C | intron_variant | ENST00000388798.7 | NP_003105.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPAG1 | ENST00000388798.7 | c.-2-321A>C | intron_variant | 1 | NM_003114.5 | ENSP00000373450.3 | ||||
SPAG1 | ENST00000251809.4 | c.-2-321A>C | intron_variant | 5 | ENSP00000251809.3 | |||||
SPAG1 | ENST00000520508.5 | c.-2-321A>C | intron_variant | 5 | ENSP00000428070.1 | |||||
SPAG1 | ENST00000520643.5 | c.-2-321A>C | intron_variant | 2 | ENSP00000427716.1 |
Frequencies
GnomAD3 genomes AF: 0.615 AC: 93411AN: 151958Hom.: 28934 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.615 AC: 93472AN: 152076Hom.: 28951 Cov.: 32 AF XY: 0.615 AC XY: 45722AN XY: 74348
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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 | GeneDx | Aug 13, 2019 | - - |
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