rs57890595

chr8-23146600-A-Cchr8-23146600-A-G

Variant summary

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

The NM_003840.5(TNFRSF10D):c.482+361T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,146 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: TNFRSF10D NM_003840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

TNFRSF10D (HGNC:11907): (TNF receptor superfamily member 10d) The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor contains an extracellular TRAIL-binding domain, a transmembrane domain, and a truncated cytoplamic death domain. This receptor does not induce apoptosis, and has been shown to play an inhibitory role in TRAIL-induced cell apoptosis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFRSF10D	NM_003840.5	c.482+361T>G		intron_variant		ENST00000312584.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFRSF10D	ENST00000312584.4	c.482+361T>G		intron_variant		1	NM_003840.5	P1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25068 AN: 152028 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.165 AC: 25119 AN: 152146 Hom.: 2409 Cov.: 32 AF XY: 0.166 AC XY: 12371 AN XY: 74392

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.174

Alfa AF: 0.0767 Hom.: 107

Bravo AF: 0.176

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.2
Dann	Benign	0.71

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: rs57890595; hg19: chr8-23004113;