rs7859473
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 0.0261 in 152,224 control chromosomes in the GnomAD database, including 104 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 0.026 ( 104 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: -0.996
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0261 (3975/152224) while in subpopulation AFR AF= 0.0248 (1029/41540). AF 95% confidence interval is 0.0235. There are 104 homozygotes in gnomad4. There are 2139 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 103 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: 0.0261 AC: 3969AN: 152108Hom.: 103 Cov.: 32
GnomAD3 genomes
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3969
AN:
152108
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Cov.:
32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4Hom.: 0 AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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AC:
0
AN:
4
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0
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0
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GnomAD4 genome ? AF: 0.0261 AC: 3975AN: 152224Hom.: 104 Cov.: 32 AF XY: 0.0287 AC XY: 2139AN XY: 74422
GnomAD4 genome
?
AF:
AC:
3975
AN:
152224
Hom.:
Cov.:
32
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2139
AN XY:
74422
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Asia WGS
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AC:
58
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