rs2864527
Positions:
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 0.0348 in 152,320 control chromosomes in the GnomAD database, including 116 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 0.035 ( 116 hom., cov: 33)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.849
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0348 (5308/152320) while in subpopulation NFE AF= 0.0411 (2795/68032). AF 95% confidence interval is 0.0398. There are 116 homozygotes in gnomad4. There are 2452 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 116 gene
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes AF: 0.0348 AC: 5296AN: 152202Hom.: 115 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0348 AC: 5308AN: 152320Hom.: 116 Cov.: 33 AF XY: 0.0329 AC XY: 2452AN XY: 74484
GnomAD4 genome
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5308
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33
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2452
AN XY:
74484
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Asia WGS
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30
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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