NM_003840.5:c.257-1114C>T

Variant names:

• chr8-23149665-G-A
• rs13257094
• NM_003840.5:c.257-1114C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003840.5(TNFRSF10D):​c.257-1114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,614 control chromosomes in the GnomAD database, including 3,767 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 0.20 (3767 hom., cov: 30)
• Consequence: TNFRSF10D NM_003840.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003840.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF10D	NM_003840.5	MANE Select	c.257-1114C>T		intron	N/A	NP_003831.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFRSF10D	ENST00000312584.4	TSL:1 MANE Select	c.257-1114C>T		intron	N/A	ENSP00000310263.3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29846 AN: 151498 Hom.: 3769 Cov.: 30

Gnomad AFR AF: 0.0500

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.197 AC: 29834 AN: 151614 Hom.: 3767 Cov.: 30 AF XY: 0.195 AC XY: 14447 AN XY: 74026

African (AFR) AF: 0.0500 AC: 2066 AN: 41354

American (AMR) AF: 0.249 AC: 3800 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3464

East Asian (EAS) AF: 0.0943 AC: 486 AN: 5156

South Asian (SAS) AF: 0.213 AC: 1017 AN: 4784

European-Finnish (FIN) AF: 0.226 AC: 2360 AN: 10432

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18264 AN: 67866

Other (OTH) AF: 0.211 AC: 444 AN: 2106

Alfa AF: 0.252 Hom.: 13257

Bravo AF: 0.192

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.98
DANN	Benign	0.45
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13257094; hg19: chr8-23007178;