rs3755480

Variant summary

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

The ENST00000243347.5(TNFAIP6):​c.232+498G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,104 control chromosomes in the GnomAD database, including 2,827 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 0.18 ( 2827 hom., cov: 32)

Consequence

TNFAIP6
ENST00000243347.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168
Variant links:
Genes affected
TNFAIP6 (HGNC:11898): (TNF alpha induced protein 6) The protein encoded by this gene is a secretory protein that contains a hyaluronan-binding domain, and thus is a member of the hyaluronan-binding protein family. The hyaluronan-binding domain is known to be involved in extracellular matrix stability and cell migration. This protein has been shown to form a stable complex with inter-alpha-inhibitor (I alpha I), and thus enhance the serine protease inhibitory activity of I alpha I, which is important in the protease network associated with inflammation. This gene can be induced by proinflammatory cytokines such as tumor necrosis factor alpha and interleukin-1. Enhanced levels of this protein are found in the synovial fluid of patients with osteoarthritis and rheumatoid arthritis.[provided by RefSeq, Dec 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNFAIP6NM_007115.4 linkuse as main transcriptc.232+498G>A intron_variant ENST00000243347.5 NP_009046.2
LOC101929319NR_110248.1 linkuse as main transcriptn.306+8217C>T intron_variant, non_coding_transcript_variant
TNFAIP6XM_047445635.1 linkuse as main transcriptc.232+498G>A intron_variant XP_047301591.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNFAIP6ENST00000243347.5 linkuse as main transcriptc.232+498G>A intron_variant 1 NM_007115.4 ENSP00000243347 P1

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27344
AN:
151986
Hom.:
2818
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.0658
Gnomad AMR
AF:
0.116
Gnomad ASJ
AF:
0.155
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.116
Gnomad FIN
AF:
0.164
Gnomad MID
AF:
0.139
Gnomad NFE
AF:
0.143
Gnomad OTH
AF:
0.159
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.180
AC:
27396
AN:
152104
Hom.:
2827
Cov.:
32
AF XY:
0.179
AC XY:
13316
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.285
Gnomad4 AMR
AF:
0.116
Gnomad4 ASJ
AF:
0.155
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.117
Gnomad4 FIN
AF:
0.164
Gnomad4 NFE
AF:
0.143
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.170
Hom.:
317
Bravo
AF:
0.183
Asia WGS
AF:
0.139
AC:
484
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.92
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs3755480; hg19: chr2-152221092; API