rs2019091
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 0.0421 in 151,170 control chromosomes in the GnomAD database, including 80 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 0.042 ( 80 hom., cov: 40)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0750
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0421 (6364/151170) while in subpopulation NFE AF= 0.0454 (3062/67468). AF 95% confidence interval is 0.044. There are 80 homozygotes in gnomad4. There are 3086 alleles in male gnomad4 subpopulation. Median coverage is 40. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 80 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: 0.0420 AC: 6350AN: 151050Hom.: 79 Cov.: 40
GnomAD3 genomes
?
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6350
AN:
151050
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Cov.:
40
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0421 AC: 6364AN: 151170Hom.: 80 Cov.: 40 AF XY: 0.0418 AC XY: 3086AN XY: 73856
GnomAD4 genome
?
AF:
AC:
6364
AN:
151170
Hom.:
Cov.:
40
AF XY:
AC XY:
3086
AN XY:
73856
Gnomad4 AFR
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Asia WGS
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AC:
87
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