Genetic Variant NM_001065.4:c.36A>G (chr12-6341779-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001065.4(TNFRSF1A):c.36A>G(p.Pro12Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,613,612 control chromosomes in the GnomAD database, including 135,701 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 12088 hom., cov: 33)

Exomes 𝑓: 0.41 ( 123613 hom. )

Consequence

TNFRSF1A
NM_001065.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts U:3B:10O:1

Conservation

PhyloP100: -0.107

Publications

161 publications found

Variant links:

Genes affected

TNFRSF1A (HGNC:11916): (TNF receptor superfamily member 1A) This gene encodes a member of the TNF receptor superfamily of proteins. The encoded receptor is found in membrane-bound and soluble forms that interact with membrane-bound and soluble forms, respectively, of its ligand, tumor necrosis factor alpha. Binding of membrane-bound tumor necrosis factor alpha to the membrane-bound receptor induces receptor trimerization and activation, which plays a role in cell survival, apoptosis, and inflammation. Proteolytic processing of the encoded receptor results in release of the soluble form of the receptor, which can interact with free tumor necrosis factor alpha to inhibit inflammation. Mutations in this gene underlie tumor necrosis factor receptor-associated periodic syndrome (TRAPS), characterized by fever, abdominal pain and other features. Mutations in this gene may also be associated with multiple sclerosis in human patients. [provided by RefSeq, Sep 2016]

TNFRSF1A Gene-Disease associations (from GenCC):

TNF receptor 1-associated periodic fever syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Illumina, Laboratory for Molecular Medicine, Ambry Genetics, PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), G2P

TNFRSF1A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 12-6341779-T-C is Benign according to our data. Variant chr12-6341779-T-C is described in ClinVar as Benign. ClinVar VariationId is 257326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.107 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001065.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TNFRSF1A	NM_001065.4	MANE Select	c.36A>G	p.Pro12Pro	synonymous	Exon 1 of 10	NP_001056.1	P19438-1
TNFRSF1A	NM_001346091.2		c.-135A>G		5_prime_UTR	Exon 1 of 9	NP_001333020.1	P19438-2
TNFRSF1A	NM_001346092.2		c.-542A>G		5_prime_UTR	Exon 1 of 11	NP_001333021.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TNFRSF1A	ENST00000162749.7	TSL:1 MANE Select	c.36A>G	p.Pro12Pro	synonymous	Exon 1 of 10	ENSP00000162749.2	P19438-1
TNFRSF1A	ENST00000540022.5	TSL:1	c.36A>G	p.Pro12Pro	synonymous	Exon 1 of 9	ENSP00000438343.1	F5H061
TNFRSF1A	ENST00000366159.9	TSL:1	n.70A>G		non_coding_transcript_exon	Exon 1 of 10

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59765

AN:

152026

Hom.:

12096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.357

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.286

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.382

GnomAD2 exomes

AF:

0.374

AC:

93640

AN:

250294

AF XY:

0.374

show subpopulations

Gnomad AFR exome

AF:

0.356

Gnomad AMR exome

AF:

0.334

Gnomad ASJ exome

AF:

0.422

Gnomad EAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.457

Gnomad NFE exome

AF:

0.429

Gnomad OTH exome

AF:

0.398

GnomAD4 exome

AF:

0.406

AC:

593442

AN:

1461468

Hom.:

123613

Cov.:

AF XY:

0.404

AC XY:

293957

AN XY:

727038

show subpopulations

African (AFR)

AF:

0.357

AC:

11934

AN:

33474

American (AMR)

AF:

0.332

AC:

14830

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.419

AC:

10935

AN:

26124

East Asian (EAS)

AF:

0.158

AC:

6257

AN:

39698

South Asian (SAS)

AF:

0.297

AC:

25600

AN:

86244

European-Finnish (FIN)

AF:

0.458

AC:

24416

AN:

53320

Middle Eastern (MID)

AF:

0.409

AC:

2354

AN:

5760

European-Non Finnish (NFE)

AF:

0.426

AC:

473415

AN:

1111736

Other (OTH)

AF:

0.392

AC:

23701

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

20042

40084

60125

80167

100209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14158

28316

42474

56632

70790

<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:

0.393

AC:

59763

AN:

152144

Hom.:

12088

Cov.:

AF XY:

0.391

AC XY:

29083

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.356

AC:

14785

AN:

41510

American (AMR)

AF:

0.364

AC:

5567

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.425

AC:

1475

AN:

3472

East Asian (EAS)

AF:

0.135

AC:

698

AN:

5166

South Asian (SAS)

AF:

0.287

AC:

1386

AN:

4830

European-Finnish (FIN)

AF:

0.461

AC:

4881

AN:

10588

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.436

AC:

29647

AN:

67976

Other (OTH)

AF:

0.380

AC:

804

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1922

3845

5767

7690

9612

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.415

Hom.:

33815

Bravo

AF:

0.383

Asia WGS

AF:

0.225

AC:

784

AN:

3478

EpiCase

AF:

0.439

EpiControl

AF:

0.432

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (5)

not provided (4)

TNF receptor-associated periodic fever syndrome (TRAPS) (2)

Associated with severe COVID-19 disease (1)

Susceptibility to severe coronavirus disease (COVID-19) (1)

Susceptibility to severe coronavirus disease (COVID-19) due to high plasma levels of TNF, TNFR, and/or TNFR7 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

(source)

DANN

Benign

0.79

PhyloP100

-0.11

PromoterAI

-0.032

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over