chr20-63696776-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003823.4(TNFRSF6B):c.9G>C(p.Ala3Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000487 in 1,437,088 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
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000049 ( 0 hom. )
Consequence
TNFRSF6B
NM_003823.4 synonymous
NM_003823.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.62
Publications
0 publications found
Genes affected
TNFRSF6B (HGNC:11921): (TNF receptor superfamily member 6b) This gene belongs to the tumor necrosis factor receptor superfamily. The encoded protein is postulated to play a regulatory role in suppressing FasL- and LIGHT-mediated cell death. It acts as a decoy receptor that competes with death receptors for ligand binding. Over-expression of this gene has been noted in gastrointestinal tract tumors. Read-through transcription into this gene from the neighboring upstream gene, which encodes regulator of telomere elongation helicase 1 (RTEL1), generates a non-coding transcript. [provided by RefSeq, Feb 2011]
RTEL1-TNFRSF6B (HGNC:44095): (RTEL1-TNFRSF6B readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring RTEL1 (regulator of telomere elongation helicase 1) and TNFRSF6B (tumor necrosis factor receptor superfamily, member 6b, decoy) genes on chromosome 20. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.059).
BP6
Variant 20-63696776-G-C is Benign according to our data. Variant chr20-63696776-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1640604.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.62 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TNFRSF6B | ENST00000369996.3 | c.9G>C | p.Ala3Ala | synonymous_variant | Exon 1 of 3 | 1 | NM_003823.4 | ENSP00000359013.1 | ||
| RTEL1-TNFRSF6B | ENST00000492259.6 | n.*1348G>C | non_coding_transcript_exon_variant | Exon 33 of 35 | 5 | ENSP00000457428.1 | ||||
| RTEL1-TNFRSF6B | ENST00000492259.6 | n.*1348G>C | 3_prime_UTR_variant | Exon 33 of 35 | 5 | ENSP00000457428.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD2 exomes AF: 0.00000919 AC: 2AN: 217560 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
217560
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000487 AC: 7AN: 1437088Hom.: 0 Cov.: 29 AF XY: 0.00000421 AC XY: 3AN XY: 712192 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1437088
Hom.:
Cov.:
29
AF XY:
AC XY:
3
AN XY:
712192
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33054
American (AMR)
AF:
AC:
0
AN:
43114
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24830
East Asian (EAS)
AF:
AC:
0
AN:
39286
South Asian (SAS)
AF:
AC:
0
AN:
83066
European-Finnish (FIN)
AF:
AC:
0
AN:
49864
Middle Eastern (MID)
AF:
AC:
0
AN:
5664
European-Non Finnish (NFE)
AF:
AC:
6
AN:
1099028
Other (OTH)
AF:
AC:
1
AN:
59182
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.432
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
34
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 30, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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