Variant rs11064 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014350.4(TNFAIP8):c.*312A>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 0.247 in 271,980 control chromosomes in the GnomAD database, including 8,658 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 0.27 ( 5460 hom., cov: 32)

Exomes 𝑓: 0.22 ( 3198 hom. )

Consequence

TNFAIP8
NM_014350.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.634

Variant links:

Genes affected

TNFAIP8 (HGNC:17260): (TNF alpha induced protein 8) Enables cysteine-type endopeptidase inhibitor activity involved in apoptotic process. Involved in positive regulation of apoptotic process. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TNFAIP8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFAIP8	NM_014350.4 linkuse as main transcript	c.*312A>G		3_prime_UTR_variant	2/2	ENST00000504771.3	NP_055165.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TNFAIP8	ENST00000504771.3 linkuse as main transcript	c.*312A>G	3_prime_UTR_variant	2/2	1	NM_014350.4	ENSP00000422245	O95379-1
TNFAIP8	ENST00000415806.2 linkuse as main transcript	c.*908A>G	3_prime_UTR_variant	3/3	1		ENSP00000408534
TNFAIP8	ENST00000503646.1 linkuse as main transcript	c.*312A>G	3_prime_UTR_variant	3/3	2		ENSP00000421848	O95379-1
TNFAIP8	ENST00000513374.1 linkuse as main transcript	c.*312A>G	3_prime_UTR_variant	2/2	2		ENSP00000427424	O95379-4

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40493

AN:

152060

Hom.:

5457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.0992

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.222

AC:

26549

AN:

119802

Hom.:

3198

Cov.:

AF XY:

0.219

AC XY:

13650

AN XY:

62380

show subpopulations

Gnomad4 AFR exome

AF:

0.230

Gnomad4 AMR exome

AF:

0.243

Gnomad4 ASJ exome

AF:

0.215

Gnomad4 EAS exome

AF:

0.0945

Gnomad4 SAS exome

AF:

0.152

Gnomad4 FIN exome

AF:

0.253

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.266

AC:

40504

AN:

152178

Hom.:

5460

Cov.:

AF XY:

0.266

AC XY:

19760

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.266

Gnomad4 AMR

AF:

0.243

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.0991

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.277

Hom.:

1458

Bravo

AF:

0.262

Asia WGS

AF:

0.149

AC:

515

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.5

DANN

Benign

0.72

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over