rs10521550
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The variant allele was found at a frequency of 0.0129 in 112,137 control chromosomes in the GnomAD database, including 16 homozygotes. There are 416 hemizygotes in GnomAD. 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 0.013 ( 16 hom., 416 hem., cov: 23)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.143
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0129 (1449/112137) while in subpopulation SAS AF= 0.0199 (54/2708). AF 95% confidence interval is 0.0178. There are 16 homozygotes in gnomad4. There are 416 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 16 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.0129 AC: 1445AN: 112086Hom.: 16 Cov.: 23 AF XY: 0.0120 AC XY: 412AN XY: 34250
GnomAD3 genomes
?
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1445
AN:
112086
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23
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412
AN XY:
34250
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0129 AC: 1449AN: 112137Hom.: 16 Cov.: 23 AF XY: 0.0121 AC XY: 416AN XY: 34311
GnomAD4 genome
?
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AC:
1449
AN:
112137
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23
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416
AN XY:
34311
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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