rs10420252
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The variant allele was found at a frequency of 0.0973 in 153,178 control chromosomes in the GnomAD database, including 785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.097 ( 776 hom., cov: 32)
Exomes 𝑓: 0.12 ( 9 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.66
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 19-35648270-G-A is Benign according to our data. Variant chr19-35648270-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 328837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.134 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: 0.0971 AC: 14778AN: 152138Hom.: 773 Cov.: 32
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GnomAD4 exome AF: 0.119 AC: 110AN: 922Hom.: 9 Cov.: 0 AF XY: 0.124 AC XY: 71AN XY: 574
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GnomAD4 genome ? AF: 0.0972 AC: 14799AN: 152256Hom.: 776 Cov.: 32 AF XY: 0.0993 AC XY: 7393AN XY: 74424
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Mitochondrial complex IV deficiency, nuclear type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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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