chr3-103172459-G-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.0157 in 152,162 control chromosomes in the GnomAD database, including 79 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 0.016 ( 79 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.564
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|
Frequencies
GnomAD3 genomes 0.0157 AC: 2388AN: 152044Hom.: 79 Cov.: 32
GnomAD3 genomes
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2388
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152044
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0157 AC: 2389AN: 152162Hom.: 79 Cov.: 32 AF XY: 0.0151 AC XY: 1127AN XY: 74400
GnomAD4 genome
AF:
AC:
2389
AN:
152162
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Cov.:
32
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AC XY:
1127
AN XY:
74400
Gnomad4 AFR
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Asia WGS
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10
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