chr1-201194177-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164586.2(IGFN1):c.31C>T(p.Pro11Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P11R) 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGFN1 | NM_001164586.2 | c.31C>T | p.Pro11Ser | 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.31C>T | p.Pro11Ser | missense_variant | Exon 3 of 24 | 5 | NM_001164586.2 | ENSP00000334714.4 | ||
IGFN1 | ENST00000437879.6 | n.31C>T | non_coding_transcript_exon_variant | Exon 3 of 26 | 1 | ENSP00000399041.2 | ||||
IGFN1 | ENST00000295591.12 | c.31C>T | p.Pro11Ser | missense_variant | Exon 3 of 25 | 5 | ENSP00000295591.9 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.31C>T (p.P11S) alteration is located in exon 3 (coding exon 2) of the IGFN1 gene. This alteration results from a C to T substitution at nucleotide position 31, causing the proline (P) at amino acid position 11 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.