1-154429209-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000565.4(IL6R):c.99C>T(p.Gly33Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,611,598 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000565.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL6R | ENST00000368485.8 | c.99C>T | p.Gly33Gly | synonymous_variant | Exon 2 of 10 | 1 | NM_000565.4 | ENSP00000357470.3 | ||
IL6R | ENST00000344086.8 | c.99C>T | p.Gly33Gly | synonymous_variant | Exon 2 of 9 | 1 | ENSP00000340589.4 | |||
IL6R | ENST00000622330.5 | c.99C>T | p.Gly33Gly | synonymous_variant | Exon 2 of 7 | 1 | ENSP00000477739.1 | |||
IL6R | ENST00000512471.1 | c.99C>T | p.Gly33Gly | synonymous_variant | Exon 2 of 4 | 4 | ENSP00000423184.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251000Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135646
GnomAD4 exome AF: 0.0000425 AC: 62AN: 1459352Hom.: 2 Cov.: 33 AF XY: 0.0000551 AC XY: 40AN XY: 725418
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74444
ClinVar
Submissions by phenotype
IL6R-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at