rs11032080

Variant names:

• chr11-4393849-T-C
• rs11032080
• ENST00000641797.5:n.70T>C

Variant summary

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

The ENST00000641797.5(ENSG00000291144):​n.70T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,920 control chromosomes in the GnomAD database, including 3,271 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 0.20 (3271 hom., cov: 31)
• Consequence: ENSG00000291144 ENST00000641797.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 7 publications found

Genes affected

ENSG00000291144 (HGNC:):

TRIM21 (HGNC:11312): (tripartite motif containing 21) This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The encoded protein is part of the RoSSA ribonucleoprotein, which includes a single polypeptide and one of four small RNA molecules. The RoSSA particle localizes to both the cytoplasm and the nucleus. RoSSA interacts with autoantigens in patients with Sjogren syndrome and systemic lupus erythematosus. Alternatively spliced transcript variants for this gene have been described but the full-length nature of only one has been determined. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM21	NM_003141.4	c.-266A>G		upstream_gene_variant		ENST00000254436.8	NP_003132.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM21	ENST00000254436.8	c.-266A>G		upstream_gene_variant		1	NM_003141.4	ENSP00000254436.7

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30172 AN: 151802 Hom.: 3269 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.199 AC: 30179 AN: 151920 Hom.: 3271 Cov.: 31 AF XY: 0.196 AC XY: 14572 AN XY: 74288

African (AFR) AF: 0.267 AC: 11056 AN: 41374

American (AMR) AF: 0.143 AC: 2182 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3468

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5166

South Asian (SAS) AF: 0.114 AC: 548 AN: 4818

European-Finnish (FIN) AF: 0.196 AC: 2071 AN: 10586

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12944 AN: 67910

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.192 Hom.: 7815

Bravo AF: 0.201

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.51
PhyloP100		0.23
PromoterAI		0.046	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11032080; hg19: chr11-4415079;