dbSNP rs2239530: TRIM26:c.*1538G>C (chr6-30184338-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003449.5(TRIM26):c.*1538G>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,210 control chromosomes in the GnomAD database, including 2,868 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 0.17 ( 2868 hom., cov: 32)

Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

TRIM26
NM_003449.5 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.798

Publications

14 publications found

Variant links:

Genes affected

TRIM26 (HGNC:12962): (tripartite motif containing 26) The protein encoded by this gene is 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 protein localizes to cytoplasmic bodies. Although the function of the protein is unknown, the RING domain suggests that the protein may have DNA-binding activity. The gene localizes to the major histocompatibility complex (MHC) class I region on chromosome 6. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jun 2011]

TRIM26 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM26	NM_003449.5 link	c.*1538G>C		downstream_gene_variant		ENST00000454678.7	NP_003440.1	Q12899A0A024RCP3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TRIM26	ENST00000454678.7 link	c.*1538G>C	downstream_gene_variant	1	NM_003449.5	ENSP00000410446.2	Q12899
TRIM26	ENST00000437089.5 link	c.*1538G>C	downstream_gene_variant	1		ENSP00000395491.1	Q12899
TRIM26	ENST00000453195.5 link	c.*1538G>C	downstream_gene_variant	1		ENSP00000391879.1	Q12899
TRIM26	ENST00000480999.1 link	n.*117G>C	downstream_gene_variant	2

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

26042

AN:

152086

Hom.:

2866

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0420

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0950

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.171

AC:

26049

AN:

152204

Hom.:

2868

Cov.:

AF XY:

0.172

AC XY:

12825

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0419

AC:

1741

AN:

41546

American (AMR)

AF:

0.190

AC:

2901

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

400

AN:

3470

East Asian (EAS)

AF:

0.208

AC:

1072

AN:

5166

South Asian (SAS)

AF:

0.0953

AC:

460

AN:

4826

European-Finnish (FIN)

AF:

0.293

AC:

3097

AN:

10568

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15808

AN:

68016

Other (OTH)

AF:

0.129

AC:

273

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1073

2146

3220

4293

5366

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<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:

0.216

Hom.:

2189

Bravo

AF:

0.158

Asia WGS

AF:

0.131

AC:

456

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.75

(source)

DANN

Benign

0.48

PhyloP100

-0.80

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over