1-201195856-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001164586.2(IGFN1):c.145C>T(p.Arg49Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000432 in 1,551,512 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001164586.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IGFN1 | NM_001164586.2 | c.145C>T | p.Arg49Trp | missense_variant | Exon 4 of 24 | ENST00000335211.9 | NP_001158058.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IGFN1 | ENST00000335211.9 | c.145C>T | p.Arg49Trp | missense_variant | Exon 4 of 24 | 5 | NM_001164586.2 | ENSP00000334714.4 | ||
IGFN1 | ENST00000437879.6 | n.145C>T | non_coding_transcript_exon_variant | Exon 4 of 26 | 1 | ENSP00000399041.2 | ||||
IGFN1 | ENST00000295591.12 | c.145C>T | p.Arg49Trp | missense_variant | Exon 4 of 25 | 5 | ENSP00000295591.9 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 25AN: 156270Hom.: 0 AF XY: 0.000181 AC XY: 15AN XY: 82832
GnomAD4 exome AF: 0.0000422 AC: 59AN: 1399210Hom.: 1 Cov.: 30 AF XY: 0.0000377 AC XY: 26AN XY: 690110
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.145C>T (p.R49W) alteration is located in exon 4 (coding exon 3) of the IGFN1 gene. This alteration results from a C to T substitution at nucleotide position 145, causing the arginine (R) at amino acid position 49 to be replaced by a tryptophan (W). 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