11-120169734-T-G

Variant names:

• chr11-120169734-T-G
• rs2444240
• ENST00000319763.1:n.173-37T>G

Variant summary

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

The ENST00000532833.1(TRIM29):​c.-115+15516A>C 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: TRIM29 ENST00000532833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 12 publications found

Genes affected

ENSG00000176984 (HGNC:):

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532833.1. 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
	LOC107984399	NR_159965.1		n.173-37T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000176984	ENST00000319763.1	TSL:1	n.173-37T>G		intron	N/A
	ENSG00000176984	ENST00000530303.5	TSL:1	n.173-37T>G		intron	N/A
	TRIM29	ENST00000532833.1	TSL:4	c.-115+15516A>C		intron	N/A	ENSP00000436567.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61887 AN: 151986 Hom.: 12722 Cov.: 34

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.: 0 AF XY: 0.427 AC XY: 52395 AN XY: 122700

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

GnomAD4 genome AF: 0.407 AC: 61904 AN: 152104 Hom.: 12721 Cov.: 34 AF XY: 0.409 AC XY: 30414 AN XY: 74366

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.69
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs2444240; hg19: chr11-120040442;