19-18175086-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006332.5(IFI30):c.179C>T(p.Pro60Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,613,836 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006332.5 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFI30 | NM_006332.5 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 7 | ENST00000407280.4 | NP_006323.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFI30 | ENST00000407280.4 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 7 | 1 | NM_006332.5 | ENSP00000384886.1 | ||
ENSG00000268173 | ENST00000593731.1 | n.*1615C>T | non_coding_transcript_exon_variant | Exon 20 of 25 | 2 | ENSP00000471914.1 | ||||
ENSG00000268173 | ENST00000593731.1 | n.*1615C>T | 3_prime_UTR_variant | Exon 20 of 25 | 2 | ENSP00000471914.1 |
Frequencies
GnomAD3 genomes AF: 0.00244 AC: 372AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00235 AC: 585AN: 248576Hom.: 2 AF XY: 0.00231 AC XY: 312AN XY: 134930
GnomAD4 exome AF: 0.00293 AC: 4288AN: 1461556Hom.: 8 Cov.: 31 AF XY: 0.00279 AC XY: 2027AN XY: 727046
GnomAD4 genome AF: 0.00244 AC: 372AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.00259 AC XY: 193AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
PIK3R2: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at