19-49890978-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152899.2(IL4I1):c.766A>G(p.Arg256Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000271 in 1,107,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152899.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL4I1 | NM_152899.2 | c.766A>G | p.Arg256Gly | missense_variant | 7/8 | ENST00000391826.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4I1 | ENST00000391826.7 | c.766A>G | p.Arg256Gly | missense_variant | 7/8 | 1 | NM_152899.2 | P2 | |
IL4I1 | ENST00000341114.7 | c.832A>G | p.Arg278Gly | missense_variant | 9/10 | 1 | A2 | ||
IL4I1 | ENST00000595948.5 | c.832A>G | p.Arg278Gly | missense_variant | 9/10 | 1 | A2 | ||
IL4I1 | ENST00000601717.5 | c.*618A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 125572Hom.: 0 Cov.: 29 FAILED QC
GnomAD3 exomes AF: 0.00000928 AC: 2AN: 215446Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119312
GnomAD4 exome AF: 0.00000271 AC: 3AN: 1107882Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 551480
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 125572Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 58838
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.832A>G (p.R278G) alteration is located in exon 9 (coding exon 6) of the IL4I1 gene. This alteration results from a A to G substitution at nucleotide position 832, causing the arginine (R) at amino acid position 278 to be replaced by a glycine (G). 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