Variant chr17-28342346-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_021137.5(TNFAIP1):c.618C>T(p.Asp206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00562 in 1,607,540 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0059 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0056 ( 71 hom. )

Consequence

TNFAIP1
NM_021137.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.83

Variant links:

Genes affected

TNFAIP1 (HGNC:11894): (TNF alpha induced protein 1) This gene was identified as a gene whose expression can be induced by the tumor necrosis factor alpha (TNF) in umbilical vein endothelial cells. Studies of a similar gene in mouse suggest that the expression of this gene is developmentally regulated in a tissue-specific manner. [provided by RefSeq, Jul 2008]

TNFAIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

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

BP6

Variant 17-28342346-C-T is Benign according to our data. Variant chr17-28342346-C-T is described in ClinVar as [Benign]. Clinvar id is 3024741.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.84 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFAIP1	NM_021137.5 linkuse as main transcript	c.618C>T	p.Asp206=	synonymous_variant	6/7	ENST00000226225.7
TNFAIP1	XM_017024993.3 linkuse as main transcript	c.618C>T	p.Asp206=	synonymous_variant	6/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP1	ENST00000226225.7 linkuse as main transcript	c.618C>T	p.Asp206=	synonymous_variant	6/7	1	NM_021137.5	P1	Q13829-1
TNFAIP1	ENST00000544907.6 linkuse as main transcript	c.306C>T	p.Asp102=	synonymous_variant	5/6	2			Q13829-2
TNFAIP1	ENST00000577535.1 linkuse as main transcript	c.306C>T	p.Asp102=	synonymous_variant	4/4	3
TNFAIP1	ENST00000583213.1 linkuse as main transcript	n.339C>T		non_coding_transcript_exon_variant	4/5	3

Frequencies

GnomAD3 genomes

AF:

0.00592

AC:

901

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000796

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00829

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0106

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00592

AC:

1489

AN:

251318

Hom.:

AF XY:

0.00571

AC XY:

776

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.000739

Gnomad AMR exome

AF:

0.00124

Gnomad ASJ exome

AF:

0.00338

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00828

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00603

GnomAD4 exome

AF:

0.00559

AC:

8138

AN:

1455198

Hom.:

Cov.:

AF XY:

0.00571

AC XY:

4129

AN XY:

722650

show subpopulations

Gnomad4 AFR exome

AF:

0.000659

Gnomad4 AMR exome

AF:

0.00114

Gnomad4 ASJ exome

AF:

0.00434

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00858

Gnomad4 NFE exome

AF:

0.00650

Gnomad4 OTH exome

AF:

0.00496

GnomAD4 genome

AF:

0.00591

AC:

901

AN:

152342

Hom.:

Cov.:

AF XY:

0.00549

AC XY:

409

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.000794

Gnomad4 AMR

AF:

0.00163

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00829

Gnomad4 NFE

AF:

0.0106

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00859

Hom.:

Bravo

AF:

0.00445

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00809

EpiControl

AF:

0.00546

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

TNFAIP1: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

5.8

DANN

Benign

0.90

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over