rs1061622
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001066.3(TNFRSF1B):āc.587T>Gā(p.Met196Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,613,590 control chromosomes in the GnomAD database, including 43,833 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001066.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF1B | NM_001066.3 | c.587T>G | p.Met196Arg | missense_variant | 6/10 | ENST00000376259.7 | NP_001057.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF1B | ENST00000376259.7 | c.587T>G | p.Met196Arg | missense_variant | 6/10 | 1 | NM_001066.3 | ENSP00000365435 | P1 | |
TNFRSF1B | ENST00000492361.1 | n.576T>G | non_coding_transcript_exon_variant | 5/9 | 1 | |||||
TNFRSF1B | ENST00000489921.1 | n.299T>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.216 AC: 32885AN: 151996Hom.: 3645 Cov.: 32
GnomAD3 exomes AF: 0.216 AC: 54148AN: 250344Hom.: 6096 AF XY: 0.221 AC XY: 29964AN XY: 135350
GnomAD4 exome AF: 0.232 AC: 338472AN: 1461476Hom.: 40176 Cov.: 37 AF XY: 0.233 AC XY: 169357AN XY: 727046
GnomAD4 genome AF: 0.216 AC: 32928AN: 152114Hom.: 3657 Cov.: 32 AF XY: 0.215 AC XY: 15954AN XY: 74358
ClinVar
Submissions by phenotype
Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR2 Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Aug 07, 2021 | Differences in plasma levels of TNFR1 and TNFR2 according to genotypes - |
Associated with severe COVID-19 disease Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Jul 01, 2023 | - - |
Susceptibility to severe coronavirus disease (COVID-19) Uncertain:1
Uncertain significance, no assertion criteria provided | research | HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas | Feb 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at