chr2-113075195-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_173161.3(IL1F10):c.290C>G(p.Thr97Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,613,536 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173161.3 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 |
---|---|---|---|---|---|---|---|
IL1F10 | NM_173161.3 | c.290C>G | p.Thr97Arg | missense_variant | 5/5 | ENST00000341010.6 | |
IL1F10 | NM_032556.6 | c.290C>G | p.Thr97Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1F10 | ENST00000341010.6 | c.290C>G | p.Thr97Arg | missense_variant | 5/5 | 1 | NM_173161.3 | P1 | |
IL1F10 | ENST00000393197.3 | c.290C>G | p.Thr97Arg | missense_variant | 4/4 | 1 | P1 | ||
IL1F10 | ENST00000496265.1 | n.356C>G | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000841 AC: 21AN: 249598Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135052
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461190Hom.: 2 Cov.: 31 AF XY: 0.0000936 AC XY: 68AN XY: 726874
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.290C>G (p.T97R) alteration is located in exon 4 (coding exon 4) of the IL1F10 gene. This alteration results from a C to G substitution at nucleotide position 290, causing the threonine (T) at amino acid position 97 to be replaced by an arginine (R). 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