rs5945642
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 0.0165 in 112,549 control chromosomes in the GnomAD database, including 28 homozygotes. There are 612 hemizygotes in GnomAD. 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 0.017 ( 28 hom., 612 hem., cov: 23)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.834
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0165 (1860/112549) while in subpopulation NFE AF= 0.0233 (1243/53326). AF 95% confidence interval is 0.0222. There are 28 homozygotes in gnomad4. There are 612 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 28 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: 0.0165 AC: 1859AN: 112496Hom.: 28 Cov.: 23 AF XY: 0.0176 AC XY: 611AN XY: 34654
GnomAD3 genomes
?
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1859
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112496
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23
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611
AN XY:
34654
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0165 AC: 1860AN: 112549Hom.: 28 Cov.: 23 AF XY: 0.0176 AC XY: 612AN XY: 34717
GnomAD4 genome
?
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AC:
1860
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112549
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23
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612
AN XY:
34717
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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