chr1-12109632-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001243.5(TNFRSF8):c.488C>T(p.Pro163Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,613,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001243.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF8 | NM_001243.5 | c.488C>T | p.Pro163Leu | missense_variant | 5/15 | ENST00000263932.7 | NP_001234.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF8 | ENST00000263932.7 | c.488C>T | p.Pro163Leu | missense_variant | 5/15 | 1 | NM_001243.5 | ENSP00000263932 | P1 | |
TNFRSF8 | ENST00000417814.3 | c.155C>T | p.Pro52Leu | missense_variant | 4/14 | 1 | ENSP00000390650 | |||
TNFRSF8 | ENST00000514649.5 | c.*232C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/14 | 1 | ENSP00000421938 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 58AN: 250930Hom.: 1 AF XY: 0.000280 AC XY: 38AN XY: 135760
GnomAD4 exome AF: 0.000183 AC: 267AN: 1461458Hom.: 0 Cov.: 31 AF XY: 0.000193 AC XY: 140AN XY: 727056
GnomAD4 genome AF: 0.000197 AC: 30AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.488C>T (p.P163L) alteration is located in exon 5 (coding exon 5) of the TNFRSF8 gene. This alteration results from a C to T substitution at nucleotide position 488, causing the proline (P) at amino acid position 163 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at