dbSNP rs12365876: ENSG00000291144:n.55T>C (chr11-4393834-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000641797.5(ENSG00000291144):n.55T>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 152,142 control chromosomes in the GnomAD database, including 3,281 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 ( 3274 hom., cov: 32)

Exomes 𝑓: 0.14 ( 7 hom. )

Consequence

ENSG00000291144
ENST00000641797.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.650

Publications

7 publications found

Variant links:

Genes affected

ENSG00000291144 (HGNC:):

ENSG00000291144 links:

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]

TRIM21 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641797.5. 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
	TRIM21	NM_003141.4	MANE Select	c.-251A>G		upstream_gene	N/A	NP_003132.2

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000291144	ENST00000641797.5	n.55T>C	non_coding_transcript_exon	Exon 1 of 3
ENSG00000291144	ENST00000685350.2	n.60T>C	non_coding_transcript_exon	Exon 1 of 3
ENSG00000291144	ENST00000687315.2	n.98T>C	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30174

AN:

151728

Hom.:

3272

Cov.:

show subpopulations

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:

0.114

Gnomad FIN

AF:

0.196

Gnomad MID

AF:

0.217

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.210

GnomAD4 exome

AF:

0.139

AC:

AN:

296

Hom.:

AF XY:

0.144

AC XY:

AN XY:

208

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.0652

AC:

AN:

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.157

AC:

AN:

210

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.199

AC:

30182

AN:

151846

Hom.:

3274

Cov.:

AF XY:

0.196

AC XY:

14567

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.268

AC:

11063

AN:

41352

American (AMR)

AF:

0.143

AC:

2180

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

725

AN:

3466

East Asian (EAS)

AF:

0.00155

AC:

AN:

5168

South Asian (SAS)

AF:

0.114

AC:

550

AN:

4814

European-Finnish (FIN)

AF:

0.196

AC:

2067

AN:

10564

Middle Eastern (MID)

AF:

0.212

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.191

AC:

12945

AN:

67914

Other (OTH)

AF:

0.208

AC:

438

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1222

2445

3667

4890

6112

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.195

Hom.:

3720

Bravo

AF:

0.201

Asia WGS

AF:

0.0780

AC:

272

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.8

(source)

DANN

Benign

0.57

PhyloP100

-0.65

PromoterAI

0.20

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over