chr1-206770949-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000572.3(IL10):c.336G>C(p.Leu112=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L112L) has been classified as Likely benign.
Frequency
Consequence
NM_000572.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL10 | NM_000572.3 | c.336G>C | p.Leu112= | synonymous_variant | 3/5 | ENST00000423557.1 | |
IL19 | NM_153758.5 | c.-278C>G | 5_prime_UTR_variant | 1/7 | ENST00000659997.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL10 | ENST00000423557.1 | c.336G>C | p.Leu112= | synonymous_variant | 3/5 | 1 | NM_000572.3 | P1 | |
IL19 | ENST00000659997.3 | c.-278C>G | 5_prime_UTR_variant | 1/7 | NM_153758.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251464Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461866Hom.: 0 Cov.: 35 AF XY: 0.00000550 AC XY: 4AN XY: 727236
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
Inflammatory bowel disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at