rs73222601

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000221132.8(TNFRSF10A):​c.306+2220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,190 control chromosomes in the GnomAD database, including 4,056 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 4056 hom., cov: 32)

Consequence

TNFRSF10A
ENST00000221132.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
Variant links:
Genes affected
TNFRSF10A (HGNC:11904): (TNF receptor superfamily member 10a) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is activated by tumor necrosis factor-related apoptosis inducing ligand (TNFSF10/TRAIL), and thus transduces cell death signal and induces cell apoptosis. Studies with FADD-deficient mice suggested that FADD, a death domain containing adaptor protein, is required for the apoptosis mediated by this protein. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNFRSF10ANM_003844.4 linkuse as main transcriptc.306+2220T>C intron_variant ENST00000221132.8 NP_003835.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNFRSF10AENST00000221132.8 linkuse as main transcriptc.306+2220T>C intron_variant 1 NM_003844.4 ENSP00000221132 P1
TNFRSF10AENST00000613472.1 linkuse as main transcriptc.31+2495T>C intron_variant 1 ENSP00000480778
TNFRSF10AENST00000524158.5 linkuse as main transcriptc.-301+1897T>C intron_variant 5 ENSP00000428884

Frequencies

GnomAD3 genomes
AF:
0.209
AC:
31834
AN:
152072
Hom.:
4051
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0622
Gnomad AMI
AF:
0.283
Gnomad AMR
AF:
0.321
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.287
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.223
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.246
Gnomad OTH
AF:
0.244
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.209
AC:
31852
AN:
152190
Hom.:
4056
Cov.:
32
AF XY:
0.214
AC XY:
15891
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.0623
Gnomad4 AMR
AF:
0.322
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.288
Gnomad4 SAS
AF:
0.395
Gnomad4 FIN
AF:
0.223
Gnomad4 NFE
AF:
0.246
Gnomad4 OTH
AF:
0.243
Alfa
AF:
0.221
Hom.:
969
Bravo
AF:
0.208
Asia WGS
AF:
0.329
AC:
1145
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.69
DANN
Benign
0.33

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs73222601; hg19: chr8-23080049; API