rs151344628
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001065.4(TNFRSF1A):c.1075C>T(p.Leu359Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000633 in 1,593,250 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001065.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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TNFRSF1A | NM_001065.4 | c.1075C>T | p.Leu359Leu | synonymous_variant | Exon 10 of 10 | ENST00000162749.7 | NP_001056.1 | |
TNFRSF1A | NM_001346091.2 | c.751C>T | p.Leu251Leu | synonymous_variant | Exon 9 of 9 | NP_001333020.1 | ||
TNFRSF1A | NM_001346092.2 | c.616C>T | p.Leu206Leu | synonymous_variant | Exon 11 of 11 | NP_001333021.1 | ||
TNFRSF1A | NR_144351.2 | n.1263C>T | non_coding_transcript_exon_variant | Exon 9 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000572 AC: 127AN: 222140Hom.: 0 AF XY: 0.000454 AC XY: 56AN XY: 123276
GnomAD4 exome AF: 0.000647 AC: 933AN: 1440942Hom.: 0 Cov.: 32 AF XY: 0.000626 AC XY: 448AN XY: 716146
GnomAD4 genome AF: 0.000499 AC: 76AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000550 AC XY: 41AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
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TNF receptor-associated periodic fever syndrome (TRAPS) Benign:1Other:1
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not specified Benign:1
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. -
Autoinflammatory syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at