chr16-3068238-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001376923.1(IL32):c.200C>T(p.Pro67Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,593,120 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict 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 Benign (★). Synonymous variant affecting the same amino acid position (i.e. P67P) has been classified as Benign.
Frequency
Consequence
NM_001376923.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.200C>T | p.Pro67Leu | missense_variant, splice_region_variant | 6/7 | ENST00000525643.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL32 | ENST00000525643.7 | c.200C>T | p.Pro67Leu | missense_variant, splice_region_variant | 6/7 | 1 | NM_001376923.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00289 AC: 440AN: 152160Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00368 AC: 784AN: 213332Hom.: 7 AF XY: 0.00382 AC XY: 438AN XY: 114664
GnomAD4 exome AF: 0.00360 AC: 5188AN: 1440842Hom.: 19 Cov.: 31 AF XY: 0.00362 AC XY: 2590AN XY: 714718
GnomAD4 genome AF: 0.00289 AC: 440AN: 152278Hom.: 2 Cov.: 32 AF XY: 0.00287 AC XY: 214AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at