chr5-55976257-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002184.4(IL6ST):āc.22C>Gā(p.Leu8Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 1,586,984 control chromosomes in the GnomAD database, including 200 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL6ST | NM_002184.4 | c.22C>G | p.Leu8Val | missense_variant | 3/17 | ENST00000381298.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL6ST | ENST00000381298.7 | c.22C>G | p.Leu8Val | missense_variant | 3/17 | 1 | NM_002184.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00813 AC: 1230AN: 151344Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.0117 AC: 2772AN: 237792Hom.: 45 AF XY: 0.0138 AC XY: 1782AN XY: 129388
GnomAD4 exome AF: 0.0123 AC: 17650AN: 1435524Hom.: 187 Cov.: 28 AF XY: 0.0132 AC XY: 9441AN XY: 714342
GnomAD4 genome AF: 0.00811 AC: 1229AN: 151460Hom.: 13 Cov.: 32 AF XY: 0.00837 AC XY: 619AN XY: 73936
ClinVar
Submissions by phenotype
IL6ST-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at