rs3093720

Variant names:

• chr17-28338742-C-A
• rs3093720
• NM_021137.5:c.-114-666C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021137.5(TNFAIP1):​c.-114-666C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 151,978 control chromosomes in the GnomAD database, including 590 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 0.076 (590 hom., cov: 29)
• Consequence: TNFAIP1 NM_021137.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021137.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP1	NM_021137.5	MANE Select	c.-114-666C>A		intron	N/A	NP_066960.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP1	ENST00000226225.7	TSL:1 MANE Select	c.-114-666C>A		intron	N/A	ENSP00000226225.2
	TNFAIP1	ENST00000544907.6	TSL:2	c.-107-1567C>A		intron	N/A	ENSP00000440749.2
	TNFAIP1	ENST00000582302.2	TSL:5	c.-114-666C>A		intron	N/A	ENSP00000464515.1

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11524 AN: 151860 Hom.: 589 Cov.: 29

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0848

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0758 AC: 11518 AN: 151978 Hom.: 590 Cov.: 29 AF XY: 0.0742 AC XY: 5514 AN XY: 74298

African (AFR) AF: 0.0225 AC: 932 AN: 41472

American (AMR) AF: 0.0691 AC: 1055 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4808

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10566

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7596 AN: 67916

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0881 Hom.: 880

Bravo AF: 0.0711

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3093720; hg19: chr17-26665768;