rs3093720

Positions:

• chr17-28338742-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFAIP1	NM_021137.5	c.-114-666C>A		intron_variant		ENST00000226225.7
TNFAIP1	XM_017024993.3	c.-114-666C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNFAIP1	ENST00000226225.7	c.-114-666C>A		intron_variant		1	NM_021137.5	P1

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

Gnomad4 AFR AF: 0.0225

Gnomad4 AMR AF: 0.0691

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0979 Hom.: 506

Bravo AF: 0.0711

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.71

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

LitVar

Other links and lift over

dbSNP: rs3093720; hg19: chr17-26665768;