chr19-49889762-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152899.2(IL4I1):c.1612T>G(p.Ser538Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,523,428 control chromosomes in the GnomAD database, including 1 homozygotes. 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.1612T>G | p.Ser538Ala | missense_variant | 8/8 | ENST00000391826.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4I1 | ENST00000391826.7 | c.1612T>G | p.Ser538Ala | missense_variant | 8/8 | 1 | NM_152899.2 | P2 | |
IL4I1 | ENST00000341114.7 | c.1678T>G | p.Ser560Ala | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000595948.5 | c.1678T>G | p.Ser560Ala | missense_variant | 10/10 | 1 | A2 | ||
IL4I1 | ENST00000601717.5 | c.*1464T>G | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000383 AC: 70AN: 182662Hom.: 0 AF XY: 0.000476 AC XY: 46AN XY: 96586
GnomAD4 exome AF: 0.000362 AC: 497AN: 1371168Hom.: 1 Cov.: 31 AF XY: 0.000421 AC XY: 283AN XY: 672250
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2022 | The c.1678T>G (p.S560A) alteration is located in exon 10 (coding exon 7) of the IL4I1 gene. This alteration results from a T to G substitution at nucleotide position 1678, causing the serine (S) at amino acid position 560 to be replaced by an alanine (A). 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