15-51083632-T-C

Variant names:

• chr15-51083632-T-C
• rs3803369
• NM_001311175.2:c.52+10912A>G

Variant summary

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

The NM_001311175.2(TNFAIP8L3):​c.52+10912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,220 control chromosomes in the GnomAD database, including 49,931 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 0.81 (49931 hom., cov: 33)
• Consequence: TNFAIP8L3 NM_001311175.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 7 publications found

Genes affected

TNFAIP8L3 (HGNC:20620): (TNF alpha induced protein 8 like 3) Predicted to enable phosphatidylinositol binding activity and phosphatidylinositol transfer activity. Predicted to be involved in several processes, including inositol lipid-mediated signaling; positive regulation of intracellular signal transduction; and positive regulation of phosphatidylinositol 3-kinase activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MIR4713HG (HGNC:53124): (MIR4713 host gene)

ENSG00000304727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001311175.2. 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
	TNFAIP8L3	NM_001311175.2	MANE Select	c.52+10912A>G		intron	N/A	NP_001298104.1
	TNFAIP8L3	NM_207381.4		c.316+10912A>G		intron	N/A	NP_997264.2
	MIR4713HG	NR_146310.1		n.194+45951T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNFAIP8L3	ENST00000637513.2	TSL:1 MANE Select	c.52+10912A>G		intron	N/A	ENSP00000489743.1
	TNFAIP8L3	ENST00000327536.5	TSL:1	c.316+10912A>G		intron	N/A	ENSP00000328016.5
	TNFAIP8L3	ENST00000649177.1		c.-87+10779A>G		intron	N/A	ENSP00000498365.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122717 AN: 152100 Hom.: 49875 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.807 AC: 122830 AN: 152220 Hom.: 49931 Cov.: 33 AF XY: 0.807 AC XY: 60085 AN XY: 74438

African (AFR) AF: 0.746 AC: 30950 AN: 41508

American (AMR) AF: 0.725 AC: 11093 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2635 AN: 3470

East Asian (EAS) AF: 0.982 AC: 5085 AN: 5178

South Asian (SAS) AF: 0.804 AC: 3882 AN: 4826

European-Finnish (FIN) AF: 0.878 AC: 9314 AN: 10604

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57210 AN: 68016

Other (OTH) AF: 0.787 AC: 1664 AN: 2114

Alfa AF: 0.820 Hom.: 88305

Bravo AF: 0.791

Asia WGS AF: 0.894 AC: 3108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		0.33
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: rs3803369; hg19: chr15-51375829;