rs12553697
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000461761.5(SPATA6L):c.*255-2694A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,248 control chromosomes in the GnomAD database, including 932 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 0.10 ( 932 hom., cov: 32)
Consequence
SPATA6L
ENST00000461761.5 intron, NMD_transcript
ENST00000461761.5 intron, NMD_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
Genes affected
SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.7).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA6L | NR_148444.2 | n.1755-2694A>G | intron_variant, non_coding_transcript_variant | ||||
SPATA6L | NR_148445.2 | n.1664-2694A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATA6L | ENST00000461761.5 | c.*255-2694A>G | intron_variant, NMD_transcript_variant | 2 | |||||
SPATA6L | ENST00000485616.5 | c.*781+8998A>G | intron_variant, NMD_transcript_variant | 2 | |||||
SPATA6L | ENST00000486047.5 | c.*1107-2694A>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15856AN: 152130Hom.: 934 Cov.: 32
GnomAD3 genomes
?
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15856
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152130
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.104 AC: 15856AN: 152248Hom.: 932 Cov.: 32 AF XY: 0.107 AC XY: 7971AN XY: 74436
GnomAD4 genome
?
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AC:
15856
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152248
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32
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7971
AN XY:
74436
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377
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at