rs3128396
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000005558.8(IFRD1):c.-182+6750G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00699 in 152,324 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0070 ( 10 hom., cov: 32)
Consequence
IFRD1
ENST00000005558.8 intron
ENST00000005558.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.31
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00699 (1064/152324) while in subpopulation AFR AF= 0.0245 (1018/41554). AF 95% confidence interval is 0.0232. There are 10 homozygotes in gnomad4. There are 517 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105375457 | XR_001745325.2 | n.3832C>T | non_coding_transcript_exon_variant | 3/3 | |||
IFRD1 | NM_001007245.3 | c.-182+6750G>A | intron_variant | ||||
IFRD1 | NM_001197080.2 | c.-57+6750G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFRD1 | ENST00000005558.8 | c.-182+6750G>A | intron_variant | 1 | P3 | ||||
IFRD1 | ENST00000432734.1 | c.-182+6750G>A | intron_variant | 4 | |||||
IFRD1 | ENST00000621379.4 | c.-57+6750G>A | intron_variant | 2 | A1 | ||||
IFRD1 | ENST00000675578.1 | c.-112+6750G>A | intron_variant | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00700 AC: 1065AN: 152206Hom.: 10 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00699 AC: 1064AN: 152324Hom.: 10 Cov.: 32 AF XY: 0.00694 AC XY: 517AN XY: 74488
GnomAD4 genome
?
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32
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517
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74488
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3478
ClinVar
Not reported inComputational scores
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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