1-201194178-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001164586.2(IGFN1):c.32C>G(p.Pro11Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00678 in 1,551,644 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P11S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164586.2 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 |
---|---|---|---|---|---|---|---|---|
IGFN1 | NM_001164586.2 | c.32C>G | p.Pro11Arg | missense_variant | Exon 3 of 24 | ENST00000335211.9 | NP_001158058.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGFN1 | ENST00000335211.9 | c.32C>G | p.Pro11Arg | missense_variant | Exon 3 of 24 | 5 | NM_001164586.2 | ENSP00000334714.4 | ||
IGFN1 | ENST00000437879.6 | n.32C>G | non_coding_transcript_exon_variant | Exon 3 of 26 | 1 | ENSP00000399041.2 | ||||
IGFN1 | ENST00000295591.12 | c.32C>G | p.Pro11Arg | missense_variant | Exon 3 of 25 | 5 | ENSP00000295591.9 |
Frequencies
GnomAD3 genomes AF: 0.00474 AC: 722AN: 152198Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00435 AC: 677AN: 155666Hom.: 1 AF XY: 0.00439 AC XY: 362AN XY: 82540
GnomAD4 exome AF: 0.00701 AC: 9805AN: 1399328Hom.: 39 Cov.: 31 AF XY: 0.00683 AC XY: 4712AN XY: 690170
GnomAD4 genome AF: 0.00474 AC: 722AN: 152316Hom.: 9 Cov.: 32 AF XY: 0.00470 AC XY: 350AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
IGFN1: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at