rs12557549
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 0.0121 in 110,785 control chromosomes in the GnomAD database, including 8 homozygotes. There are 375 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 0.012 ( 8 hom., 375 hem., cov: 22)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.00
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0121 (1345/110785) while in subpopulation AMR AF= 0.02 (208/10388). AF 95% confidence interval is 0.0178. There are 8 homozygotes in gnomad4. There are 375 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
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Frequencies
GnomAD3 genomes AF: 0.0122 AC: 1348AN: 110733Hom.: 8 Cov.: 22 AF XY: 0.0114 AC XY: 375AN XY: 33035
GnomAD3 genomes
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1348
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110733
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22
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375
AN XY:
33035
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0121 AC: 1345AN: 110785Hom.: 8 Cov.: 22 AF XY: 0.0113 AC XY: 375AN XY: 33097
GnomAD4 genome
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1345
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110785
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22
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375
AN XY:
33097
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at