rs3733403
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The variant allele was found at a frequency of 0.18 in 152,142 control chromosomes in the GnomAD database, including 3,185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.18 ( 3185 hom., cov: 33)
Failed GnomAD Quality Control
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.264
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 4-186265981-C-G is Benign according to our data. Variant chr4-186265981-C-G is described in ClinVar as [Benign]. Clinvar id is 348368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-186265981-C-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
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Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 27394AN: 152022Hom.: 3185 Cov.: 33
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33
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSRAC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
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0
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0
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0
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GnomAD4 genome ? AF: 0.180 AC: 27417AN: 152142Hom.: 3185 Cov.: 33 AF XY: 0.182 AC XY: 13514AN XY: 74376
GnomAD4 genome
?
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27417
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152142
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33
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13514
AN XY:
74376
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Asia WGS
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745
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary factor XI deficiency disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at