5-132484285-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002198.3(IRF1):c.853+77G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,517,494 control chromosomes in the GnomAD database, including 85,718 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002198.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRF1 | ENST00000245414.9 | c.853+77G>A | intron_variant | Intron 9 of 9 | 1 | NM_002198.3 | ENSP00000245414.4 | |||
ENSG00000283782 | ENST00000640655.2 | c.-637-1907C>T | intron_variant | Intron 1 of 25 | 5 | ENSP00000491596.2 |
Frequencies
GnomAD3 genomes AF: 0.376 AC: 56982AN: 151372Hom.: 11071 Cov.: 31
GnomAD4 exome AF: 0.327 AC: 447316AN: 1366004Hom.: 74633 Cov.: 23 AF XY: 0.329 AC XY: 222980AN XY: 678514
GnomAD4 genome AF: 0.377 AC: 57039AN: 151490Hom.: 11085 Cov.: 31 AF XY: 0.375 AC XY: 27764AN XY: 73982
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 58% of patients studied by a panel of primary immunodeficiencies. Number of patients: 51. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at