rs10484479

Variant names:

• chr6-111555782-T-C
• rs10484479
• NM_147686.4:c.*3623A>G

Variant summary

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

The NM_147686.4(TRAF3IP2):​c.*3623A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,228 control chromosomes in the GnomAD database, including 743 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 0.082 (743 hom., cov: 32)
• Consequence: TRAF3IP2 NM_147686.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 8 publications found

Genes affected

TRAF3IP2 (HGNC:1343): (TRAF3 interacting protein 2) This gene encodes a protein involved in regulating responses to cytokines by members of the Rel/NF-kappaB transcription factor family. These factors play a central role in innate immunity in response to pathogens, inflammatory signals and stress. This gene product interacts with TRAF proteins (tumor necrosis factor receptor-associated factors) and either I-kappaB kinase or MAP kinase to activate either NF-kappaB or Jun kinase. Several alternative transcripts encoding different isoforms have been identified. Another transcript, which does not encode a protein and is transcribed in the opposite orientation, has been identified. Overexpression of this transcript has been shown to reduce expression of at least one of the protein encoding transcripts, suggesting it has a regulatory role in the expression of this gene. [provided by RefSeq, Aug 2009]

TRAF3IP2-AS1 (HGNC:40005): (TRAF3IP2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_147686.4. 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
	TRAF3IP2	NM_147686.4	MANE Select	c.*3623A>G		3_prime_UTR	Exon 9 of 9	NP_679211.2
	TRAF3IP2	NM_147200.3		c.*3623A>G		3_prime_UTR	Exon 10 of 10	NP_671733.2
	TRAF3IP2	NM_001164281.3		c.*3623A>G		3_prime_UTR	Exon 9 of 9	NP_001157753.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF3IP2	ENST00000368761.11	TSL:1 MANE Select	c.*3623A>G		3_prime_UTR	Exon 9 of 9	ENSP00000357750.5
	TRAF3IP2-AS1	ENST00000438298.8	TSL:2	n.251-18839T>C		intron	N/A
	TRAF3IP2-AS1	ENST00000440395.1	TSL:3	n.211-20580T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12473 AN: 152110 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0819 AC: 12467 AN: 152228 Hom.: 743 Cov.: 32 AF XY: 0.0853 AC XY: 6346 AN XY: 74428

African (AFR) AF: 0.0187 AC: 779 AN: 41548

American (AMR) AF: 0.0613 AC: 937 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.0592 AC: 307 AN: 5184

South Asian (SAS) AF: 0.0877 AC: 424 AN: 4832

European-Finnish (FIN) AF: 0.182 AC: 1934 AN: 10598

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.108 AC: 7361 AN: 67998

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0914 Hom.: 1695

Bravo AF: 0.0698

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs10484479; hg19: chr6-111876985;