Genetic Variant TNFRSF10D:c.371-44A>G (chr8-23147116-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003840.5(TNFRSF10D):c.371-44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,539,050 control chromosomes in the GnomAD database, including 89,699 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 0.36 ( 11006 hom., cov: 31)

Exomes 𝑓: 0.32 ( 78693 hom. )

Consequence

TNFRSF10D
NM_003840.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

19 publications found

Variant links:

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]

TNFRSF10D links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFRSF10D	NM_003840.5 link	c.371-44A>G		intron_variant	Intron 3 of 8	ENST00000312584.4	NP_003831.2	Q9UBN6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFRSF10D	ENST00000312584.4 link	c.371-44A>G		intron_variant	Intron 3 of 8	1	NM_003840.5	ENSP00000310263.3		Q9UBN6

Frequencies

GnomAD3 genomes

AF:

0.358

AC:

54426

AN:

151822

Hom.:

10988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.376

GnomAD2 exomes

AF:

0.382

AC:

95255

AN:

249314

AF XY:

0.370

show subpopulations

Gnomad AFR exome

AF:

0.421

Gnomad AMR exome

AF:

0.584

Gnomad ASJ exome

AF:

0.200

Gnomad EAS exome

AF:

0.827

Gnomad FIN exome

AF:

0.265

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.330

GnomAD4 exome

AF:

0.316

AC:

438197

AN:

1387110

Hom.:

78693

Cov.:

AF XY:

0.315

AC XY:

219013

AN XY:

694298

show subpopulations

African (AFR)

AF:

0.415

AC:

13207

AN:

31822

American (AMR)

AF:

0.570

AC:

25324

AN:

44464

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

5002

AN:

25590

East Asian (EAS)

AF:

0.835

AC:

32753

AN:

39202

South Asian (SAS)

AF:

0.371

AC:

31356

AN:

84562

European-Finnish (FIN)

AF:

0.267

AC:

14006

AN:

52402

Middle Eastern (MID)

AF:

0.230

AC:

1244

AN:

5404

European-Non Finnish (NFE)

AF:

0.283

AC:

296018

AN:

1045842

Other (OTH)

AF:

0.334

AC:

19287

AN:

57822

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

13883

27767

41650

55534

69417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9940

19880

29820

39760

49700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.359

AC:

54502

AN:

151940

Hom.:

11006

Cov.:

AF XY:

0.365

AC XY:

27083

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.416

AC:

17217

AN:

41384

American (AMR)

AF:

0.482

AC:

7370

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.205

AC:

711

AN:

3466

East Asian (EAS)

AF:

0.836

AC:

4322

AN:

5170

South Asian (SAS)

AF:

0.404

AC:

1947

AN:

4814

European-Finnish (FIN)

AF:

0.256

AC:

2705

AN:

10574

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.281

AC:

19070

AN:

67942

Other (OTH)

AF:

0.378

AC:

796

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1643

3287

4930

6574

8217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.312

Hom.:

28180

Bravo

AF:

0.382

Asia WGS

AF:

0.574

AC:

1993

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

(source)

DANN

Benign

0.46

PhyloP100

-1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over