5-150847809-TTTTG-TTTTGTTTG
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001145805.2(IRGM):c.-307_-304dupGTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000289 in 276,740 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 26)
Exomes 𝑓: 0.0000080 ( 0 hom. )
Consequence
IRGM
NM_001145805.2 5_prime_UTR
NM_001145805.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.876
Genes affected
IRGM (HGNC:29597): (immunity related GTPase M) This gene encodes a member of the p47 immunity-related GTPase family. The encoded protein may play a role in the innate immune response by regulating autophagy formation in response to intracellular pathogens. Polymorphisms that affect the normal expression of this gene are associated with a susceptibility to Crohn's disease and tuberculosis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRGM | NM_001145805.2 | c.-307_-304dupGTTT | 5_prime_UTR_variant | 2/2 | ENST00000522154.2 | NP_001139277.1 | ||
IRGM | NM_001346557.2 | c.-307_-304dupGTTT | 5_prime_UTR_variant | 2/4 | NP_001333486.1 | |||
IRGM | NR_170598.1 | n.809_812dupGTTT | non_coding_transcript_exon_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRGM | ENST00000522154 | c.-307_-304dupGTTT | 5_prime_UTR_variant | 2/2 | 1 | NM_001145805.2 | ENSP00000428220.1 |
Frequencies
GnomAD3 genomes AF: 0.0000462 AC: 7AN: 151528Hom.: 0 Cov.: 26
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GnomAD4 exome AF: 0.00000799 AC: 1AN: 125212Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 65620
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GnomAD4 genome AF: 0.0000462 AC: 7AN: 151528Hom.: 0 Cov.: 26 AF XY: 0.0000676 AC XY: 5AN XY: 73924
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at