dbSNP rs7776346: TRAF3IP2-AS1:n.248-34459G>A (chr6-111540162-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000438298.7(TRAF3IP2-AS1):n.248-34459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,094 control chromosomes in the GnomAD database, including 17,732 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 0.41 ( 17732 hom., cov: 32)

Consequence

TRAF3IP2-AS1
ENST00000438298.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.490

Variant links:

Genes affected

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

TRAF3IP2-AS1 links:

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TRAF3IP2-AS1	NR_034108.1 link	n.195-34459G>A	intron_variant	Intron 1 of 3
TRAF3IP2-AS1	NR_034109.1 link	n.194+56497G>A	intron_variant	Intron 1 of 1
TRAF3IP2-AS1	NR_034110.1 link	n.195-34459G>A	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TRAF3IP2-AS1	ENST00000438298.7 link	n.248-34459G>A	intron_variant	Intron 2 of 3	2
TRAF3IP2-AS1	ENST00000440395.1 link	n.211-36200G>A	intron_variant	Intron 1 of 1	3
TRAF3IP2-AS1	ENST00000442928.6 link	n.117-34459G>A	intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62951

AN:

151976

Hom.:

17682

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.580

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.362

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

GnomAD4 genome

AF:

0.415

AC:

63061

AN:

152094

Hom.:

17732

Cov.:

AF XY:

0.420

AC XY:

31219

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.788

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.244

Gnomad4 EAS

AF:

0.580

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.309

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.367

Alfa

AF:

0.251

Hom.:

12198

Bravo

AF:

0.433

Asia WGS

AF:

0.491

AC:

1708

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.54

DANN

Benign

0.41

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