chr8-23028402-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_003842.5(TNFRSF10B):āc.677T>Cā(p.Ile226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003842.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF10B | NM_003842.5 | c.677T>C | p.Ile226Thr | missense_variant | 5/9 | ENST00000276431.9 | |
TNFRSF10B | NM_147187.3 | c.590T>C | p.Ile197Thr | missense_variant | 6/10 | ||
TNFRSF10B | NR_027140.2 | n.621T>C | non_coding_transcript_exon_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF10B | ENST00000276431.9 | c.677T>C | p.Ile226Thr | missense_variant | 5/9 | 1 | NM_003842.5 | P2 | |
TNFRSF10B | ENST00000347739.3 | c.590T>C | p.Ile197Thr | missense_variant | 6/10 | 1 | A2 | ||
TNFRSF10B | ENST00000518531.5 | n.427T>C | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
TNFRSF10B | ENST00000523504.5 | c.*211T>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251488Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727248
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.590T>C (p.I197T) alteration is located in exon 6 (coding exon 6) of the TNFRSF10B gene. This alteration results from a T to C substitution at nucleotide position 590, causing the isoleucine (I) at amino acid position 197 to be replaced by a threonine (T). 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