rs12775535
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 0.0288 in 152,262 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 0.029 ( 79 hom., cov: 32)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00400
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0288 (4391/152262) while in subpopulation AFR AF= 0.0484 (2012/41552). AF 95% confidence interval is 0.0467. There are 79 homozygotes in gnomad4. There are 2065 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 79 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: 0.0288 AC: 4382AN: 152144Hom.: 77 Cov.: 32
GnomAD3 genomes
?
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4382
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152144
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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 ? AF: 0.0288 AC: 4391AN: 152262Hom.: 79 Cov.: 32 AF XY: 0.0277 AC XY: 2065AN XY: 74456
GnomAD4 genome
?
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AC:
4391
AN:
152262
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Cov.:
32
AF XY:
AC XY:
2065
AN XY:
74456
Gnomad4 AFR
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Asia WGS
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30
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