16-3067372-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001376923.1(IL32):c.16-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000715 in 1,525,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001376923.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.16-5C>T | splice_region_variant, intron_variant | Intron 2 of 6 | ENST00000525643.7 | NP_001363852.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151492Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000473 AC: 9AN: 190400Hom.: 0 AF XY: 0.0000496 AC XY: 5AN XY: 100824
GnomAD4 exome AF: 0.0000779 AC: 107AN: 1373948Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 53AN XY: 676398
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151492Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73930
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at