Genetic Variant TNFAIP8:c.*210C>T (chr5-119393591-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014350.4(TNFAIP8):c.*210C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 549,590 control chromosomes in the GnomAD database, including 21,243 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 0.30 ( 6968 hom., cov: 33)

Exomes 𝑓: 0.26 ( 14275 hom. )

Consequence

TNFAIP8
NM_014350.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486

Publications

54 publications found

Variant links:

Genes affected

TNFAIP8 (HGNC:17260): (TNF alpha induced protein 8) Enables cysteine-type endopeptidase inhibitor activity involved in apoptotic process. Involved in positive regulation of apoptotic process. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TNFAIP8 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014350.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TNFAIP8	NM_014350.4	MANE Select	c.*210C>T	3_prime_UTR	Exon 2 of 2	NP_055165.2
TNFAIP8	NM_001286814.1		c.*210C>T	3_prime_UTR	Exon 2 of 2	NP_001273743.1
TNFAIP8	NM_001286813.2		c.*210C>T	3_prime_UTR	Exon 3 of 3	NP_001273742.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TNFAIP8	ENST00000504771.3	TSL:1 MANE Select	c.*210C>T	3_prime_UTR	Exon 2 of 2	ENSP00000422245.1
TNFAIP8	ENST00000415806.2	TSL:1	c.*806C>T	3_prime_UTR	Exon 3 of 3	ENSP00000408534.2
TNFAIP8	ENST00000513374.1	TSL:2	c.*210C>T	3_prime_UTR	Exon 2 of 2	ENSP00000427424.1

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45426

AN:

151938

Hom.:

6957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.301

GnomAD4 exome

AF:

0.263

AC:

104537

AN:

397534

Hom.:

14275

Cov.:

AF XY:

0.262

AC XY:

54685

AN XY:

208954

show subpopulations

African (AFR)

AF:

0.350

AC:

4019

AN:

11498

American (AMR)

AF:

0.267

AC:

4209

AN:

15792

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

3027

AN:

12078

East Asian (EAS)

AF:

0.133

AC:

3548

AN:

26630

South Asian (SAS)

AF:

0.235

AC:

9393

AN:

39930

European-Finnish (FIN)

AF:

0.302

AC:

6830

AN:

22596

Middle Eastern (MID)

AF:

0.235

AC:

402

AN:

1708

European-Non Finnish (NFE)

AF:

0.275

AC:

67178

AN:

244462

Other (OTH)

AF:

0.260

AC:

5931

AN:

22840

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

3480

6960

10440

13920

17400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.299

AC:

45469

AN:

152056

Hom.:

6968

Cov.:

AF XY:

0.300

AC XY:

22307

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.359

AC:

14894

AN:

41466

American (AMR)

AF:

0.257

AC:

3932

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

909

AN:

3468

East Asian (EAS)

AF:

0.132

AC:

684

AN:

5178

South Asian (SAS)

AF:

0.244

AC:

1177

AN:

4818

European-Finnish (FIN)

AF:

0.326

AC:

3440

AN:

10560

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19331

AN:

67958

Other (OTH)

AF:

0.298

AC:

631

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1640

3280

4919

6559

8199

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

456

912

1368

1824

2280

<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:

0.286

Hom.:

9112

Bravo

AF:

0.297

Asia WGS

AF:

0.196

AC:

679

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.8

(source)

DANN

Benign

0.47

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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