rs717925
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 0.0124 in 152,332 control chromosomes in the GnomAD database, including 21 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 0.012 ( 21 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0150
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0124 (1882/152332) while in subpopulation NFE AF= 0.0188 (1279/68026). AF 95% confidence interval is 0.0179. There are 21 homozygotes in gnomad4. There are 884 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 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: 0.0124 AC: 1885AN: 152214Hom.: 22 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1885
AN:
152214
Hom.:
Cov.:
33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0124 AC: 1882AN: 152332Hom.: 21 Cov.: 33 AF XY: 0.0119 AC XY: 884AN XY: 74486
GnomAD4 genome
?
AF:
AC:
1882
AN:
152332
Hom.:
Cov.:
33
AF XY:
AC XY:
884
AN XY:
74486
Gnomad4 AFR
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Asia WGS
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AC:
30
AN:
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