1-201194249-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001164586.2(IGFN1):c.103C>G(p.Pro35Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000129 in 1,399,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P35P) has been classified as Likely benign.
Frequency
Consequence
NM_001164586.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGFN1 | NM_001164586.2 | c.103C>G | p.Pro35Ala | 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.103C>G | p.Pro35Ala | missense_variant | Exon 3 of 24 | 5 | NM_001164586.2 | ENSP00000334714.4 | ||
IGFN1 | ENST00000437879.6 | n.103C>G | non_coding_transcript_exon_variant | Exon 3 of 26 | 1 | ENSP00000399041.2 | ||||
IGFN1 | ENST00000295591.12 | c.103C>G | p.Pro35Ala | missense_variant | Exon 3 of 25 | 5 | ENSP00000295591.9 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 16AN: 154494Hom.: 0 AF XY: 0.0000610 AC XY: 5AN XY: 81980
GnomAD4 exome AF: 0.0000129 AC: 18AN: 1399276Hom.: 0 Cov.: 31 AF XY: 0.00000580 AC XY: 4AN XY: 690144
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.103C>G (p.P35A) alteration is located in exon 3 (coding exon 2) of the IGFN1 gene. This alteration results from a C to G substitution at nucleotide position 103, causing the proline (P) at amino acid position 35 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at