14-77027747-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_024496.4(IRF2BPL):c.46C>T(p.Leu16=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000137 in 1,603,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
IRF2BPL
NM_024496.4 synonymous
NM_024496.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.86
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 14-77027747-G-A is Benign according to our data. Variant chr14-77027747-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3039890.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0000197 (3/152162) while in subpopulation AMR AF= 0.000131 (2/15280). AF 95% confidence interval is 0.0000226. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRF2BPL | NM_024496.4 | c.46C>T | p.Leu16= | synonymous_variant | 1/1 | ENST00000238647.5 | NP_078772.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRF2BPL | ENST00000238647.5 | c.46C>T | p.Leu16= | synonymous_variant | 1/1 | NM_024496.4 | ENSP00000238647 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000255 AC: 6AN: 235190Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128792
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GnomAD4 exome AF: 0.0000131 AC: 19AN: 1450926Hom.: 0 Cov.: 34 AF XY: 0.0000111 AC XY: 8AN XY: 722104
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
IRF2BPL-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at