Genetic Variant ENSG00000176984:n.173-37T>G (chr11-120169734-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000319763.1(ENSG00000176984):n.173-37T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 372,942 control chromosomes in the GnomAD database, including 33,208 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 ( 12721 hom., cov: 34)

Exomes 𝑓: 0.43 ( 20487 hom. )

Consequence

ENSG00000176984
ENST00000319763.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690

Publications

12 publications found

Variant links:

Genes affected

ENSG00000176984 (HGNC:):

ENSG00000176984 links:

TRIM29 (HGNC:17274): (tripartite motif containing 29) The protein encoded by this gene belongs to the TRIM protein family. It has multiple zinc finger motifs and a leucine zipper motif. It has been proposed to form homo- or heterodimers which are involved in nucleic acid binding. Thus, it may act as a transcriptional regulatory factor involved in carcinogenesis and/or differentiation. It may also function in the suppression of radiosensitivity since it is associated with ataxia telangiectasia phenotype. [provided by RefSeq, Jul 2008]

TRIM29 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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984399	NR_159965.1 link	n.173-37T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000176984	ENST00000319763.1 link	n.173-37T>G	intron_variant	Intron 1 of 1	1
ENSG00000176984	ENST00000530303.5 link	n.173-37T>G	intron_variant	Intron 1 of 1	1
ENSG00000176984	ENST00000724911.1 link	n.40T>G	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61887

AN:

151986

Hom.:

12722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.514

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.433

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.427

Gnomad OTH

AF:

0.409

GnomAD4 exome

AF:

0.426

AC:

94131

AN:

220838

Hom.:

20487

Cov.:

AF XY:

0.427

AC XY:

52395

AN XY:

122700

show subpopulations

African (AFR)

AF:

0.367

AC:

2121

AN:

5782

American (AMR)

AF:

0.468

AC:

6782

AN:

14500

Ashkenazi Jewish (ASJ)

AF:

0.427

AC:

2209

AN:

5176

East Asian (EAS)

AF:

0.232

AC:

1977

AN:

8516

South Asian (SAS)

AF:

0.449

AC:

20669

AN:

46010

European-Finnish (FIN)

AF:

0.461

AC:

4392

AN:

9524

Middle Eastern (MID)

AF:

0.380

AC:

829

AN:

2182

European-Non Finnish (NFE)

AF:

0.428

AC:

50746

AN:

118682

Other (OTH)

AF:

0.421

AC:

4406

AN:

10466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

2909

5818

8727

11636

14545

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.407

AC:

61904

AN:

152104

Hom.:

12721

Cov.:

AF XY:

0.409

AC XY:

30414

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.369

AC:

15329

AN:

41502

American (AMR)

AF:

0.406

AC:

6203

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

1503

AN:

3472

East Asian (EAS)

AF:

0.241

AC:

1244

AN:

5162

South Asian (SAS)

AF:

0.443

AC:

2134

AN:

4822

European-Finnish (FIN)

AF:

0.477

AC:

5050

AN:

10592

Middle Eastern (MID)

AF:

0.414

AC:

121

AN:

292

European-Non Finnish (NFE)

AF:

0.427

AC:

29001

AN:

67956

Other (OTH)

AF:

0.403

AC:

850

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1922

3844

5767

7689

9611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

586

1172

1758

2344

2930

<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:

0.411

Hom.:

12102

Bravo

AF:

0.401

Asia WGS

AF:

0.334

AC:

1163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.2

(source)

DANN

Benign

0.69

PhyloP100

-0.069

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