chr19-49890280-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152899.2(IL4I1):c.1094G>T(p.Arg365Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000627 in 1,595,234 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.1094G>T | p.Arg365Leu | missense_variant | 8/8 | ENST00000391826.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4I1 | ENST00000391826.7 | c.1094G>T | p.Arg365Leu | missense_variant | 8/8 | 1 | NM_152899.2 | P2 | |
IL4I1 | ENST00000341114.7 | c.1160G>T | p.Arg387Leu | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000595948.5 | c.1160G>T | p.Arg387Leu | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000601717.5 | c.*946G>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152210Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1442906Hom.: 0 Cov.: 32 AF XY: 0.00000279 AC XY: 2AN XY: 716520
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2021 | The c.1160G>T (p.R387L) alteration is located in exon 10 (coding exon 7) of the IL4I1 gene. This alteration results from a G to T substitution at nucleotide position 1160, causing the arginine (R) at amino acid position 387 to be replaced by a leucine (L). 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