rs20576
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000221132.8(TNFRSF10A):āc.683A>Cā(p.Glu228Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,605,418 control chromosomes in the GnomAD database, including 28,771 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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
ENST00000221132.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF10A | NM_003844.4 | c.683A>C | p.Glu228Ala | missense_variant | 5/10 | ENST00000221132.8 | NP_003835.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF10A | ENST00000221132.8 | c.683A>C | p.Glu228Ala | missense_variant | 5/10 | 1 | NM_003844.4 | ENSP00000221132 | P1 | |
TNFRSF10A | ENST00000613472.1 | c.209A>C | p.Glu70Ala | missense_variant | 4/9 | 1 | ENSP00000480778 | |||
TNFRSF10A | ENST00000524158.5 | c.77A>C | p.Glu26Ala | missense_variant | 5/7 | 5 | ENSP00000428884 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21716AN: 151290Hom.: 1965 Cov.: 31
GnomAD3 exomes AF: 0.151 AC: 38009AN: 251454Hom.: 3544 AF XY: 0.155 AC XY: 21075AN XY: 135904
GnomAD4 exome AF: 0.185 AC: 269208AN: 1454004Hom.: 26806 Cov.: 53 AF XY: 0.183 AC XY: 132429AN XY: 723542
GnomAD4 genome AF: 0.143 AC: 21712AN: 151414Hom.: 1965 Cov.: 31 AF XY: 0.144 AC XY: 10647AN XY: 73964
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 18, 2020 | This variant is associated with the following publications: (PMID: 21484799, 23658636, 22401174) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at