Genetic Variant NM_006291.4:c.*1873G>T (chr14-103137233-G-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.*1873G>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 0.148 in 152,318 control chromosomes in the GnomAD database, including 2,098 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 0.15 ( 2098 hom., cov: 33)

Exomes 𝑓: 0.085 ( 0 hom. )

Consequence

TNFAIP2
NM_006291.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0840

Publications

8 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:

Genome browser will be placed here

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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP2	NM_006291.4 link	c.*1873G>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000560869.6	NP_006282.2	Q03169

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TNFAIP2	ENST00000560869.6 link	c.*1873G>T	3_prime_UTR_variant	Exon 12 of 12	5	NM_006291.4	ENSP00000452634.2	Q03169
TNFAIP2	ENST00000333007.8 link	c.*1873G>T	3_prime_UTR_variant	Exon 13 of 13	1		ENSP00000332326.1	Q03169
TNFAIP2	ENST00000561217.1 link	n.404G>T	non_coding_transcript_exon_variant	Exon 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22451

AN:

152058

Hom.:

2096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0803

Gnomad FIN

AF:

0.0931

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.0845

AC:

AN:

142

Hom.:

Cov.:

AF XY:

0.0750

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.143

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0889

AC:

AN:

Other (OTH)

AF:

0.143

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.148

AC:

22483

AN:

152176

Hom.:

2098

Cov.:

AF XY:

0.145

AC XY:

10782

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.264

AC:

10942

AN:

41486

American (AMR)

AF:

0.115

AC:

1754

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

432

AN:

3472

East Asian (EAS)

AF:

0.000967

AC:

AN:

5172

South Asian (SAS)

AF:

0.0803

AC:

388

AN:

4830

European-Finnish (FIN)

AF:

0.0931

AC:

987

AN:

10602

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7597

AN:

68002

Other (OTH)

AF:

0.127

AC:

268

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

958

1917

2875

3834

4792

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.128

Hom.:

578

Bravo

AF:

0.154

Asia WGS

AF:

0.0460

AC:

163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.3

(source)

DANN

Benign

0.83

PhyloP100

0.084

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