1-206768519-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000572.3(IL10):c.*117T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 695,764 control chromosomes in the GnomAD database, including 64,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_000572.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.*117T>C | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000423557.1 | NP_000563.1 | ||
IL10 | NM_001382624.1 | c.*117T>C | 3_prime_UTR_variant | Exon 3 of 3 | NP_001369553.1 | |||
IL10 | NR_168466.1 | n.951T>C | non_coding_transcript_exon_variant | Exon 6 of 6 | ||||
IL10 | NR_168467.1 | n.481T>C | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.417 AC: 63370AN: 151816Hom.: 13979 Cov.: 31
GnomAD4 exome AF: 0.408 AC: 221827AN: 543830Hom.: 50042 Cov.: 4 AF XY: 0.401 AC XY: 118071AN XY: 294534
GnomAD4 genome AF: 0.418 AC: 63439AN: 151934Hom.: 14000 Cov.: 31 AF XY: 0.410 AC XY: 30441AN XY: 74266
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 34% of patients studied by a panel of primary immunodeficiencies. Number of patients: 33. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at