X-105744956-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017416.2(IL1RAPL2):c.1049-4004T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 111,223 control chromosomes in the GnomAD database, including 869 homozygotes. There are 4,394 hemizygotes in GnomAD. 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
Consequence
NM_017416.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RAPL2 | NM_017416.2 | c.1049-4004T>C | intron_variant | ENST00000372582.6 | |||
LOC105373303 | XR_938493.3 | n.357-19453A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAPL2 | ENST00000372582.6 | c.1049-4004T>C | intron_variant | 1 | NM_017416.2 | P1 | |||
IL1RAPL2 | ENST00000485671.1 | n.44-4004T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.137 AC: 15192AN: 111167Hom.: 873 Cov.: 22 AF XY: 0.131 AC XY: 4386AN XY: 33373
GnomAD4 genome AF: 0.137 AC: 15195AN: 111223Hom.: 869 Cov.: 22 AF XY: 0.131 AC XY: 4394AN XY: 33439
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at