rs17882988

chr1-12182813-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001066.3(TNFRSF1B):c.79-5983G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,292 control chromosomes in the GnomAD database, including 1,286 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 0.12 (1286 hom., cov: 33)
• Consequence: TNFRSF1B NM_001066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.69

Genes affected

TNFRSF1B (HGNC:11917): (TNF receptor superfamily member 1B) The protein encoded by this gene is a member of the TNF-receptor superfamily. This protein and TNF-receptor 1 form a heterocomplex that mediates the recruitment of two anti-apoptotic proteins, c-IAP1 and c-IAP2, which possess E3 ubiquitin ligase activity. The function of IAPs in TNF-receptor signalling is unknown, however, c-IAP1 is thought to potentiate TNF-induced apoptosis by the ubiquitination and degradation of TNF-receptor-associated factor 2, which mediates anti-apoptotic signals. Knockout studies in mice also suggest a role of this protein in protecting neurons from apoptosis by stimulating antioxidative pathways. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFRSF1B	NM_001066.3	c.79-5983G>A		intron_variant		ENST00000376259.7
TNFRSF1B	XM_011542060.3	c.79-5983G>A		intron_variant
TNFRSF1B	XM_011542063.3	c.79-5983G>A		intron_variant
TNFRSF1B	XM_047429422.1	c.79-5983G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFRSF1B	ENST00000376259.7	c.79-5983G>A		intron_variant		1	NM_001066.3	P1
TNFRSF1B	ENST00000536782.2	c.79-5983G>A		intron_variant		1
TNFRSF1B	ENST00000492361.1	n.168-8144G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17671 AN: 152174 Hom.: 1288 Cov.: 33

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.128

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.116 AC: 17669 AN: 152292 Hom.: 1286 Cov.: 33 AF XY: 0.116 AC XY: 8650 AN XY: 74456

Gnomad4 AFR AF: 0.0362

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.127

Alfa AF: 0.135 Hom.: 325

Bravo AF: 0.110

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.50
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs17882988; hg19: chr1-12242870;