rs1561296
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001100423.2(SPATS2L):c.788+2610T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,048 control chromosomes in the GnomAD database, including 16,024 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 0.43 ( 16024 hom., cov: 31)
Consequence
SPATS2L
NM_001100423.2 intron
NM_001100423.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.168
Genes affected
SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.788+2610T>C | intron_variant | ENST00000409140.8 | |||
LOC101927741 | XR_007088047.1 | n.662+5982A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.788+2610T>C | intron_variant | 2 | NM_001100423.2 | P1 | |||
ENST00000655656.1 | n.567-11857A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.434 AC: 65870AN: 151930Hom.: 16020 Cov.: 31
GnomAD3 genomes
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65870
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151930
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.433 AC: 65880AN: 152048Hom.: 16024 Cov.: 31 AF XY: 0.435 AC XY: 32319AN XY: 74340
GnomAD4 genome
?
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AC:
65880
AN:
152048
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31
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AC XY:
32319
AN XY:
74340
Gnomad4 AFR
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Asia WGS
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1088
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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