rs1991300
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001385016.1(ATOSA):c.16+1457A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 152,218 control chromosomes in the GnomAD database, including 746 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 0.078 ( 746 hom., cov: 32)
Consequence
ATOSA
NM_001385016.1 intron
NM_001385016.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0960
Genes affected
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATOSA | NM_001385016.1 | c.16+1457A>G | intron_variant | ENST00000619572.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATOSA | ENST00000619572.5 | c.16+1457A>G | intron_variant | 1 | NM_001385016.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0780 AC: 11860AN: 152100Hom.: 744 Cov.: 32
GnomAD3 genomes
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11860
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152100
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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: 0.0780 AC: 11873AN: 152218Hom.: 746 Cov.: 32 AF XY: 0.0789 AC XY: 5869AN XY: 74426
GnomAD4 genome
?
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11873
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152218
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32
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5869
AN XY:
74426
Gnomad4 AFR
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Asia WGS
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443
AN:
3466
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