rs16860674
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 0.015 in 152,240 control chromosomes in the GnomAD database, including 62 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 0.015 ( 62 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.573
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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 afr. gnomad4 allele frequency = 0.015 (2279/152240) while in subpopulation AFR AF= 0.0518 (2152/41568). AF 95% confidence interval is 0.0499. There are 62 homozygotes in gnomad4. There are 1102 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
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Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2267AN: 152122Hom.: 61 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2267
AN:
152122
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Cov.:
32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0150 AC: 2279AN: 152240Hom.: 62 Cov.: 32 AF XY: 0.0148 AC XY: 1102AN XY: 74448
GnomAD4 genome
?
AF:
AC:
2279
AN:
152240
Hom.:
Cov.:
32
AF XY:
AC XY:
1102
AN XY:
74448
Gnomad4 AFR
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Asia WGS
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AC:
15
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