2-113118054-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173841.3(IL1RN):c.10+26T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,608,216 control chromosomes in the GnomAD database, including 56,563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_173841.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | NM_173841.3 | c.10+26T>C | intron_variant | Intron 1 of 5 | NP_776213.1 | |||
IL1RN | NM_000577.5 | c.10+26T>C | intron_variant | Intron 1 of 4 | NP_000568.1 | |||
IL1RN | NM_001318914.2 | c.-273+26T>C | intron_variant | Intron 1 of 6 | NP_001305843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206.9 | c.10+26T>C | intron_variant | Intron 1 of 5 | 1 | ENSP00000259206.5 | ||||
IL1RN | ENST00000354115.6 | c.10+26T>C | intron_variant | Intron 1 of 4 | 1 | ENSP00000329072.3 | ||||
IL1RN | ENST00000361779.7 | c.-210+26T>C | intron_variant | Intron 1 of 5 | 1 | ENSP00000354816.3 |
Frequencies
GnomAD3 genomes AF: 0.209 AC: 31842AN: 152112Hom.: 4091 Cov.: 33
GnomAD3 exomes AF: 0.253 AC: 63648AN: 251392Hom.: 9031 AF XY: 0.256 AC XY: 34797AN XY: 135884
GnomAD4 exome AF: 0.261 AC: 380615AN: 1455984Hom.: 52466 Cov.: 30 AF XY: 0.261 AC XY: 189326AN XY: 724622
GnomAD4 genome AF: 0.209 AC: 31857AN: 152232Hom.: 4097 Cov.: 33 AF XY: 0.212 AC XY: 15801AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 49% of patients studied by a panel of primary immunodeficiencies. Number of patients: 47. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at