rs6518275
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142854.2(SPATC1L):c.193+2720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0688 in 152,300 control chromosomes in the GnomAD database, including 1,139 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 0.069 ( 1139 hom., cov: 33)
Consequence
SPATC1L
NM_001142854.2 intron
NM_001142854.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.706
Genes affected
SPATC1L (HGNC:1298): (spermatogenesis and centriole associated 1 like) Enables identical protein binding activity. Predicted to act upstream of or within several processes, including actin polymerization or depolymerization; positive regulation of cAMP-dependent protein kinase activity; and positive regulation of protein kinase A signaling. Predicted to be located in sperm connecting piece. Predicted to be active in centrosome. [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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATC1L | NM_001142854.2 | c.193+2720G>A | intron_variant | ENST00000291672.6 | |||
SPATC1L | NM_032261.5 | c.-270+4452G>A | intron_variant | ||||
SPATC1L | XM_005261188.6 | c.193+2720G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATC1L | ENST00000291672.6 | c.193+2720G>A | intron_variant | 2 | NM_001142854.2 | P1 | |||
SPATC1L | ENST00000330205.10 | c.-270+4452G>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0688 AC: 10468AN: 152182Hom.: 1139 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0688 AC: 10475AN: 152300Hom.: 1139 Cov.: 33 AF XY: 0.0659 AC XY: 4906AN XY: 74482
GnomAD4 genome
?
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10475
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33
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4906
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74482
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39
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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