rs7776346

Variant names:

• chr6-111540162-G-A
• rs7776346
• ENST00000438298.8:n.251-34459G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438298.8(TRAF3IP2-AS1):​n.251-34459G>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 ENST00000438298.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438298.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF3IP2-AS1	NR_034108.1		n.195-34459G>A		intron	N/A
	TRAF3IP2-AS1	NR_034109.1		n.194+56497G>A		intron	N/A
	TRAF3IP2-AS1	NR_034110.1		n.195-34459G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRAF3IP2-AS1	ENST00000438298.8	TSL:2	n.251-34459G>A		intron	N/A
	TRAF3IP2-AS1	ENST00000440395.1	TSL:3	n.211-36200G>A		intron	N/A
	TRAF3IP2-AS1	ENST00000442928.6	TSL:4	n.117-34459G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62951 AN: 151976 Hom.: 17682 Cov.: 32

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.: 32 AF XY: 0.420 AC XY: 31219 AN XY: 74354

African (AFR) AF: 0.788 AC: 32661 AN: 41468

American (AMR) AF: 0.380 AC: 5806 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3472

East Asian (EAS) AF: 0.580 AC: 3000 AN: 5176

South Asian (SAS) AF: 0.380 AC: 1834 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3266 AN: 10568

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14559 AN: 67980

Other (OTH) AF: 0.367 AC: 776 AN: 2114

Alfa AF: 0.284 Hom.: 27375

Bravo AF: 0.433

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7776346;

hg19: chr6-111861365;