4-119322356-T-C
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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 0.566 in 386,000 control chromosomes in the GnomAD database, including 62,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.57 ( 24456 hom., cov: 32)
Exomes 𝑓: 0.57 ( 37804 hom. )
Consequence
Unknown
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.598
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 4-119322356-T-C is Benign according to our data. Variant chr4-119322356-T-C is described in ClinVar as [Benign]. Clinvar id is 1268685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.
Transcripts
RefSeq
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Ensembl
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Frequencies
GnomAD3 genomes AF: 0.567 AC: 86053AN: 151814Hom.: 24423 Cov.: 32
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GnomAD4 exome AF: 0.566 AC: 132408AN: 234068Hom.: 37804 Cov.: 0 AF XY: 0.565 AC XY: 67952AN XY: 120234
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GnomAD4 genome AF: 0.567 AC: 86151AN: 151932Hom.: 24456 Cov.: 32 AF XY: 0.564 AC XY: 41868AN XY: 74244
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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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