7-112455988-A-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001550.4(IFRD1):c.200-14A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0267 in 1,556,428 control chromosomes in the GnomAD database, including 668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.022 ( 59 hom., cov: 33)
Exomes 𝑓: 0.027 ( 609 hom. )
Consequence
IFRD1
NM_001550.4 intron
NM_001550.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.456
Genes affected
IFRD1 (HGNC:5456): (interferon related developmental regulator 1) This gene is an immediate early gene that encodes a protein related to interferon-gamma. This protein may function as a transcriptional co-activator/repressor that controls the growth and differentiation of specific cell types during embryonic development and tissue regeneration. Mutations in this gene are associated with sensory/motor neuropathy with ataxia. This gene may also be involved in modulating the pathogenesis of cystic fibrosis lung disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 7-112455988-A-C is Benign according to our data. Variant chr7-112455988-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1284865.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-112455988-A-C is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0222 (3382/152202) while in subpopulation NFE AF= 0.0342 (2323/68000). AF 95% confidence interval is 0.033. There are 59 homozygotes in gnomad4. There are 1584 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 59 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFRD1 | NM_001550.4 | c.200-14A>C | intron_variant | ENST00000403825.8 | NP_001541.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFRD1 | ENST00000403825.8 | c.200-14A>C | intron_variant | 1 | NM_001550.4 | ENSP00000384477.3 | ||||
ENSG00000288640 | ENST00000676282.1 | n.200-14A>C | intron_variant | ENSP00000501830.1 |
Frequencies
GnomAD3 genomes AF: 0.0223 AC: 3384AN: 152084Hom.: 59 Cov.: 33
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GnomAD3 exomes AF: 0.0214 AC: 5362AN: 250050Hom.: 84 AF XY: 0.0219 AC XY: 2961AN XY: 135398
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GnomAD4 exome AF: 0.0271 AC: 38109AN: 1404226Hom.: 609 Cov.: 25 AF XY: 0.0266 AC XY: 18700AN XY: 702260
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GnomAD4 genome AF: 0.0222 AC: 3382AN: 152202Hom.: 59 Cov.: 33 AF XY: 0.0213 AC XY: 1584AN XY: 74400
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at