Genetic Variant TNFAIP2:c.*1872C>T (chr14-103137232-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_006291.4(TNFAIP2):c.*1872C>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 0.633 in 152,108 control chromosomes in the GnomAD database, including 30,712 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 0.63 ( 30712 hom., cov: 33)

Exomes 𝑓: 0.66 ( 36 hom. )

Failed GnomAD Quality Control

Consequence

TNFAIP2
NM_006291.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.812

Publications

36 publications found

Variant links:

Genes affected

TNFAIP2 (HGNC:11895): (TNF alpha induced protein 2) This gene was identified as a gene whose expression can be induced by the tumor necrosis factor alpha (TNF) in umbilical vein endothelial cells. The expression of this gene was shown to be induced by retinoic acid in a cell line expressing a oncogenic version of the retinoic acid receptor alpha fusion protein, which suggested that this gene may be a retinoic acid target gene in acute promyelocytic leukemia. [provided by RefSeq, Jul 2008]

TNFAIP2 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TNFAIP2	NM_006291.4	MANE Select	c.*1872C>T	3_prime_UTR	Exon 12 of 12	NP_006282.2
TNFAIP2	NM_001371220.1		c.*1229C>T	3_prime_UTR	Exon 13 of 13	NP_001358149.1	H0YKR7
TNFAIP2	NM_001371221.1		c.*1229C>T	3_prime_UTR	Exon 13 of 13	NP_001358150.1	H0YKR7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TNFAIP2	ENST00000560869.6	TSL:5 MANE Select	c.*1872C>T	3_prime_UTR	Exon 12 of 12	ENSP00000452634.2	Q03169
TNFAIP2	ENST00000333007.8	TSL:1	c.*1872C>T	3_prime_UTR	Exon 13 of 13	ENSP00000332326.1	Q03169
TNFAIP2	ENST00000903839.1		c.*1872C>T	3_prime_UTR	Exon 14 of 14	ENSP00000573898.1

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

96136

AN:

151992

Hom.:

30684

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.821

Gnomad AMR

AF:

0.580

Gnomad ASJ

AF:

0.710

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.627

Gnomad FIN

AF:

0.543

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.666

Gnomad OTH

AF:

0.660

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.656

AC:

105

AN:

160

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.682

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.571

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.660

AC:

AN:

100

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.633

AC:

96211

AN:

152108

Hom.:

30712

Cov.:

AF XY:

0.623

AC XY:

46324

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.607

AC:

25198

AN:

41496

American (AMR)

AF:

0.580

AC:

8851

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.710

AC:

2463

AN:

3470

East Asian (EAS)

AF:

0.642

AC:

3321

AN:

5176

South Asian (SAS)

AF:

0.626

AC:

3022

AN:

4824

European-Finnish (FIN)

AF:

0.543

AC:

5731

AN:

10564

Middle Eastern (MID)

AF:

0.575

AC:

169

AN:

294

European-Non Finnish (NFE)

AF:

0.666

AC:

45305

AN:

67990

Other (OTH)

AF:

0.664

AC:

1402

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1847

3695

5542

7390

9237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.723

Hom.:

19679

Bravo

AF:

0.637

Asia WGS

AF:

0.713

AC:

2476

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.6

(source)

DANN

Benign

0.73

PhyloP100

-0.81

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over