chr16-3067377-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001376923.1(IL32):c.16G>A(p.Val6Ile) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,538,538 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 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 (★).
Frequency
Consequence
NM_001376923.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.16G>A | p.Val6Ile | missense_variant, splice_region_variant | 3/7 | ENST00000525643.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL32 | ENST00000525643.7 | c.16G>A | p.Val6Ile | missense_variant, splice_region_variant | 3/7 | 1 | NM_001376923.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00730 AC: 1105AN: 151426Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00231 AC: 454AN: 196390Hom.: 4 AF XY: 0.00168 AC XY: 175AN XY: 104342
GnomAD4 exome AF: 0.000678 AC: 940AN: 1386994Hom.: 13 Cov.: 32 AF XY: 0.000599 AC XY: 409AN XY: 683060
GnomAD4 genome ? AF: 0.00739 AC: 1120AN: 151544Hom.: 17 Cov.: 32 AF XY: 0.00705 AC XY: 522AN XY: 74008
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at