NM_001311175.2:c.-109_-101dupCGCCGCCCG

Variant names:

• chr15-51094695-C-CCGGGCGGCG
• rs201887319
• NM_001311175.2:c.-109_-101dupCGCCGCCCG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001311175.2(TNFAIP8L3):​c.-109_-101dupCGCCGCCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000532 in 1,062,408 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00061 (2 hom., cov: 27)
  • Exomes 𝑓: 0.00052 (2 hom.)
• Consequence: TNFAIP8L3 NM_001311175.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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)

LOC124903491 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TNFAIP8L3	NM_001311175.2	c.-109_-101dupCGCCGCCCG		5_prime_UTR_variant	Exon 1 of 2	ENST00000637513.2	NP_001298104.1
TNFAIP8L3	NM_207381.4	c.173-17_173-9dupCGCCGCCCG		intron_variant	Intron 1 of 2		NP_997264.2
MIR4713HG	NR_146310.1	n.194+57029_194+57037dupGGCGCGGGC		intron_variant	Intron 1 of 2
LOC124903491	XR_007064631.1	n.-248_-247insCGGGCGGCG		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TNFAIP8L3	ENST00000637513.2	c.-109_-101dupCGCCGCCCG		5_prime_UTR_variant	Exon 1 of 2	1	NM_001311175.2	ENSP00000489743.1
TNFAIP8L3	ENST00000327536.5	c.173-17_173-9dupCGCCGCCCG		intron_variant	Intron 1 of 2	1		ENSP00000328016.5
MIR4713HG	ENST00000559909.1	n.194+57029_194+57037dupGGCGCGGGC		intron_variant	Intron 1 of 2	4
TNFAIP8L3	ENST00000649177.1	c.-380_-372dupCGCCGCCCG		upstream_gene_variant				ENSP00000498365.1

Frequencies

GnomAD3 genomes AF: 0.000606 AC: 89 AN: 146826 Hom.: 2 Cov.: 27

Gnomad AFR AF: 0.000342

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00115

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000393

Gnomad SAS AF: 0.00291

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.000560

Gnomad OTH AF: 0.000987

GnomAD4 exome AF: 0.000519 AC: 475 AN: 915474 Hom.: 2 Cov.: 4 AF XY: 0.000554 AC XY: 238 AN XY: 429590

Gnomad4 AFR exome AF: 0.000112

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000130

Gnomad4 EAS exome AF: 0.000105

Gnomad4 SAS exome AF: 0.00369

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000450

Gnomad4 OTH exome AF: 0.000653

GnomAD4 genome AF: 0.000613 AC: 90 AN: 146934 Hom.: 2 Cov.: 27 AF XY: 0.000503 AC XY: 36 AN XY: 71506

Gnomad4 AFR AF: 0.000341

Gnomad4 AMR AF: 0.00115

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.00312

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000560

Gnomad4 OTH AF: 0.000977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201887319; hg19: chr15-51386892;