Variant 15-51094695-CCGGGCGGCG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000637513.2(TNFAIP8L3):c.-109_-101del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,061,794 control chromosomes in the GnomAD database, including 29,898 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 3403 hom., cov: 27)

Exomes 𝑓: 0.23 ( 26495 hom. )

Consequence

TNFAIP8L3
ENST00000637513.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0750

Variant links:

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]

TNFAIP8L3 links:

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

MIR4713HG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 15-51094695-CCGGGCGGCG-C is Benign according to our data. Variant chr15-51094695-CCGGGCGGCG-C is described in ClinVar as [Benign]. Clinvar id is 768709.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
TNFAIP8L3	NM_001311175.2 linkuse as main transcript	c.-109_-101del	5_prime_UTR_variant	1/2	ENST00000637513.2	NP_001298104.1
MIR4713HG	NR_146310.1 linkuse as main transcript	n.194+57029_194+57037del	intron_variant, non_coding_transcript_variant
TNFAIP8L3	NM_207381.4 linkuse as main transcript	c.173-17_173-9del	splice_polypyrimidine_tract_variant, intron_variant			NP_997264.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
TNFAIP8L3	ENST00000637513.2 linkuse as main transcript	c.-109_-101del	5_prime_UTR_variant	1/2	1	NM_001311175.2	ENSP00000489743	P1
TNFAIP8L3	ENST00000327536.5 linkuse as main transcript	c.173-17_173-9del	splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000328016
MIR4713HG	ENST00000559909.1 linkuse as main transcript	n.194+57029_194+57037del	intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

29484

AN:

146750

Hom.:

3403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.142

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.173

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.237

AC:

AN:

350

Hom.:

AF XY:

0.221

AC XY:

AN XY:

204

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad SAS exome

AF:

0.0833

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.245

Gnomad OTH exome

AF:

0.125

GnomAD4 exome

AF:

0.231

AC:

211797

AN:

914936

Hom.:

26495

AF XY:

0.231

AC XY:

99157

AN XY:

429334

show subpopulations

Gnomad4 AFR exome

AF:

0.0885

Gnomad4 AMR exome

AF:

0.160

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.323

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.221

GnomAD4 genome

AF:

0.201

AC:

29482

AN:

146858

Hom.:

3403

Cov.:

AF XY:

0.200

AC XY:

14286

AN XY:

71460

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.205

Gnomad4 ASJ

AF:

0.157

Gnomad4 EAS

AF:

0.435

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.105

Hom.:

178

Bravo

AF:

0.197

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over