rs10518384

Variant names:

• chr4-121178365-G-C
• rs10518384
• NM_001244764.2:c.210+4311C>G

Variant summary

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

The NM_001244764.2(TNIP3):​c.210+4311C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 152,292 control chromosomes in the GnomAD database, including 321 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 0.051 (321 hom., cov: 32)
• Consequence: TNIP3 NM_001244764.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 0 publications found

Genes affected

TNIP3 (HGNC:19315): (TNFAIP3 interacting protein 3) Enables polyubiquitin modification-dependent protein binding activity. Involved in cellular response to lipopolysaccharide; negative regulation of I-kappaB kinase/NF-kappaB signaling; and toll-like receptor signaling pathway. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001244764.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNIP3	NM_001244764.2		c.210+4311C>G		intron	N/A	NP_001231693.1	Q96KP6-3
	TNIP3	NM_001128843.2		c.189+4311C>G		intron	N/A	NP_001122315.2	Q96KP6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TNIP3	ENST00000509841.1	TSL:2	c.210+4311C>G		intron	N/A	ENSP00000426613.1	Q96KP6-3
	TNIP3	ENST00000507879.5	TSL:2	c.189+4311C>G		intron	N/A	ENSP00000427106.1	Q96KP6-2
	TNIP3	ENST00000868872.1		c.-22+4311C>G		intron	N/A	ENSP00000538931.1

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7801 AN: 152174 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0158

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0514 AC: 7829 AN: 152292 Hom.: 321 Cov.: 32 AF XY: 0.0530 AC XY: 3948 AN XY: 74468

African (AFR) AF: 0.105 AC: 4374 AN: 41550

American (AMR) AF: 0.0469 AC: 718 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5190

South Asian (SAS) AF: 0.0156 AC: 75 AN: 4820

European-Finnish (FIN) AF: 0.0671 AC: 712 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1689 AN: 68032

Other (OTH) AF: 0.0398 AC: 84 AN: 2110

Alfa AF: 0.0419 Hom.: 26

Bravo AF: 0.0530

Asia WGS AF: 0.0250 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10518384; hg19: chr4-122099520;