rs66994812
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 0.0242 in 152,270 control chromosomes in the GnomAD database, including 61 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 0.024 ( 61 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.612
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0242 (3689/152270) while in subpopulation AFR AF= 0.0361 (1499/41548). AF 95% confidence interval is 0.0346. There are 61 homozygotes in gnomad4. There are 1713 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 61 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: 0.0243 AC: 3690AN: 152152Hom.: 61 Cov.: 32
GnomAD3 genomes
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AF:
AC:
3690
AN:
152152
Hom.:
Cov.:
32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
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0
AN:
6
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Cov.:
0
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0
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6
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GnomAD4 genome ? AF: 0.0242 AC: 3689AN: 152270Hom.: 61 Cov.: 32 AF XY: 0.0230 AC XY: 1713AN XY: 74456
GnomAD4 genome
?
AF:
AC:
3689
AN:
152270
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Cov.:
32
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AC XY:
1713
AN XY:
74456
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Asia WGS
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AC:
38
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