NM_001145805.2:c.313C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001145805.2(IRGM):c.313C>T(p.Leu105Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,551,610 control chromosomes in the GnomAD database, including 18,592 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001145805.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRGM | NM_001145805.2 | c.313C>T | p.Leu105Leu | synonymous_variant | Exon 2 of 2 | ENST00000522154.2 | NP_001139277.1 | |
IRGM | NM_001346557.2 | c.313C>T | p.Leu105Leu | synonymous_variant | Exon 2 of 4 | NP_001333486.1 | ||
IRGM | NR_170598.1 | n.1428C>T | non_coding_transcript_exon_variant | Exon 2 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.207 AC: 31482AN: 152052Hom.: 5243 Cov.: 32
GnomAD3 exomes AF: 0.165 AC: 25447AN: 154216Hom.: 3159 AF XY: 0.164 AC XY: 13452AN XY: 81810
GnomAD4 exome AF: 0.109 AC: 153155AN: 1399440Hom.: 13335 Cov.: 33 AF XY: 0.111 AC XY: 76783AN XY: 690246
GnomAD4 genome AF: 0.207 AC: 31535AN: 152170Hom.: 5257 Cov.: 32 AF XY: 0.207 AC XY: 15406AN XY: 74394
ClinVar
Submissions by phenotype
Inflammatory bowel disease 19 Pathogenic:1Benign:1
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not specified Benign:1
While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.646, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at