rs10404453
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_108100.1(SPACA6-AS1):n.222C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 647,306 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0091 ( 16 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 9 hom. )
Consequence
SPACA6-AS1
NR_108100.1 non_coding_transcript_exon
NR_108100.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.127
Genes affected
SPACA6-AS1 (HGNC:49383): (SPACA6 antisense RNA 1)
SPACA6 (HGNC:27113): (sperm acrosome associated 6) Predicted to be involved in fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]
MIR125A (HGNC:31505): (microRNA 125a) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00912 (1387/152040) while in subpopulation AFR AF= 0.0312 (1296/41474). AF 95% confidence interval is 0.0298. There are 16 homozygotes in gnomad4. There are 639 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPACA6-AS1 | NR_108100.1 | n.222C>T | non_coding_transcript_exon_variant | 1/2 | |||
SPACA6 | NM_001316994.2 | c.92-1243G>A | intron_variant | ||||
SPACA6 | XM_017026300.3 | c.-41-1243G>A | intron_variant | ||||
MIR125A | NR_029693.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPACA6-AS1 | ENST00000602324.1 | n.222C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
SPACA6 | ENST00000646845.1 | c.368-1243G>A | intron_variant | ||||||
SPACA6 | ENST00000710615.1 | c.-41-1243G>A | intron_variant | A2 | |||||
MIR125A | ENST00000385273.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00906 AC: 1376AN: 151920Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00261 AC: 475AN: 182214Hom.: 9 AF XY: 0.00185 AC XY: 179AN XY: 96816
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GnomAD4 exome AF: 0.00142 AC: 703AN: 495266Hom.: 9 Cov.: 0 AF XY: 0.00114 AC XY: 303AN XY: 265192
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GnomAD4 genome ? AF: 0.00912 AC: 1387AN: 152040Hom.: 16 Cov.: 32 AF XY: 0.00860 AC XY: 639AN XY: 74310
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at