rs6465787
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 0.014 in 151,842 control chromosomes in the GnomAD database, including 48 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 0.014 ( 48 hom., cov: 31)
Consequence
Unknown
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.419
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.014 (2132/151842) while in subpopulation AFR AF= 0.0466 (1927/41360). AF 95% confidence interval is 0.0449. There are 48 homozygotes in gnomad4. There are 1015 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 48 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: 0.0140 AC: 2125AN: 151724Hom.: 48 Cov.: 31
GnomAD3 genomes
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2125
AN:
151724
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0140 AC: 2132AN: 151842Hom.: 48 Cov.: 31 AF XY: 0.0137 AC XY: 1015AN XY: 74242
GnomAD4 genome
?
AF:
AC:
2132
AN:
151842
Hom.:
Cov.:
31
AF XY:
AC XY:
1015
AN XY:
74242
Gnomad4 AFR
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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