19-49889845-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152899.2(IL4I1):c.1529C>A(p.Pro510His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000315 in 1,587,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL4I1 | NM_152899.2 | c.1529C>A | p.Pro510His | missense_variant | 8/8 | ENST00000391826.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4I1 | ENST00000391826.7 | c.1529C>A | p.Pro510His | missense_variant | 8/8 | 1 | NM_152899.2 | P2 | |
IL4I1 | ENST00000341114.7 | c.1595C>A | p.Pro532His | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000595948.5 | c.1595C>A | p.Pro532His | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000601717.5 | c.*1381C>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000866 AC: 2AN: 230830Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125298
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1434750Hom.: 0 Cov.: 32 AF XY: 0.00000141 AC XY: 1AN XY: 711302
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1595C>A (p.P532H) alteration is located in exon 10 (coding exon 7) of the IL4I1 gene. This alteration results from a C to A substitution at nucleotide position 1595, causing the proline (P) at amino acid position 532 to be replaced by a histidine (H). 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