rs3851228

Variant names:

• chr6-111526988-A-T
• rs3851228
• ENST00000438298.8:n.250+42127A>T

Variant summary

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

The ENST00000438298.8(TRAF3IP2-AS1):​n.250+42127A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 151,678 control chromosomes in the GnomAD database, including 907 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 0.094 (907 hom., cov: 31)
• Consequence: TRAF3IP2-AS1 ENST00000438298.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 47 publications found

Genes affected

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

LOC107986522 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRAF3IP2-AS1	NR_034108.1	n.194+43323A>T		intron_variant	Intron 1 of 3
TRAF3IP2-AS1	NR_034109.1	n.194+43323A>T		intron_variant	Intron 1 of 1
TRAF3IP2-AS1	NR_034110.1	n.194+43323A>T		intron_variant	Intron 1 of 2
LOC107986522	XR_001743809.2	n.6224-752T>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRAF3IP2-AS1	ENST00000438298.8	n.250+42127A>T		intron_variant	Intron 2 of 3	2
TRAF3IP2-AS1	ENST00000440395.1	n.210+42127A>T		intron_variant	Intron 1 of 1	3
TRAF3IP2-AS1	ENST00000442928.6	n.116+43323A>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0942 AC: 14275 AN: 151566 Hom.: 906 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0943 AC: 14302 AN: 151678 Hom.: 907 Cov.: 31 AF XY: 0.0921 AC XY: 6832 AN XY: 74146

African (AFR) AF: 0.173 AC: 7155 AN: 41274

American (AMR) AF: 0.0681 AC: 1038 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3460

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5174

South Asian (SAS) AF: 0.0486 AC: 234 AN: 4812

European-Finnish (FIN) AF: 0.0563 AC: 589 AN: 10466

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4394 AN: 67944

Other (OTH) AF: 0.101 AC: 213 AN: 2108

Alfa AF: 0.0834 Hom.: 94

Bravo AF: 0.0998

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3851228; hg19: chr6-111848191;