rs61270113
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001145805.2(IRGM):c.-935G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,054 control chromosomes in the GnomAD database, including 5,175 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 0.21 ( 5175 hom., cov: 32)
Exomes 𝑓: 0.050 ( 0 hom. )
Consequence
IRGM
NM_001145805.2 5_prime_UTR
NM_001145805.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.146
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRGM | NM_001145805.2 | c.-935G>A | 5_prime_UTR_variant | 1/2 | ENST00000522154.2 | ||
IRGM | NM_001346557.2 | c.-935G>A | 5_prime_UTR_variant | 1/4 | |||
IRGM | NR_170598.1 | n.181G>A | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRGM | ENST00000522154.2 | c.-935G>A | 5_prime_UTR_variant | 1/2 | 1 | NM_001145805.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.206 AC: 31210AN: 151612Hom.: 5161 Cov.: 32
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GnomAD4 exome AF: 0.0497 AC: 16AN: 322Hom.: 0 Cov.: 0 AF XY: 0.0444 AC XY: 11AN XY: 248
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GnomAD4 genome ? AF: 0.206 AC: 31262AN: 151732Hom.: 5175 Cov.: 32 AF XY: 0.206 AC XY: 15298AN XY: 74188
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ClinVar
Not reported inComputational 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