rs8103142
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_172139.4(IFNL3):āc.209A>Gā(p.Lys70Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,562,762 control chromosomes in the GnomAD database, including 85,144 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 Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_172139.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNL3 | NM_172139.4 | c.209A>G | p.Lys70Arg | missense_variant | 2/5 | ENST00000413851.3 | |
IFNL3 | NM_001346937.2 | c.221A>G | p.Lys74Arg | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNL3 | ENST00000413851.3 | c.209A>G | p.Lys70Arg | missense_variant | 2/5 | 1 | NM_172139.4 | A2 | |
IFNL3 | ENST00000613087.5 | c.221A>G | p.Lys74Arg | missense_variant | 3/6 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.396 AC: 60034AN: 151586Hom.: 13742 Cov.: 30
GnomAD3 exomes AF: 0.289 AC: 65750AN: 227246Hom.: 11485 AF XY: 0.279 AC XY: 34364AN XY: 123294
GnomAD4 exome AF: 0.300 AC: 423987AN: 1411058Hom.: 71362 Cov.: 36 AF XY: 0.297 AC XY: 208467AN XY: 701368
GnomAD4 genome AF: 0.396 AC: 60121AN: 151704Hom.: 13782 Cov.: 30 AF XY: 0.387 AC XY: 28678AN XY: 74092
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at