rs2084898

Positions:

• chr11-120156040-G-A
• chr11-120156040-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532833.1(TRIM29):​c.-114-17895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 152,192 control chromosomes in the GnomAD database, including 819 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 0.093 (819 hom., cov: 33)
• Consequence: TRIM29 ENST00000532833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM29	ENST00000529040.1	c.-114-17895C>T		intron_variant		4		ENSP00000433084
TRIM29	ENST00000532833.1	c.-114-17895C>T		intron_variant		4		ENSP00000436567

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14168 AN: 152076 Hom.: 819 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0604

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0931 AC: 14173 AN: 152192 Hom.: 819 Cov.: 33 AF XY: 0.0913 AC XY: 6794 AN XY: 74390

Gnomad4 AFR AF: 0.0396

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.119

Alfa AF: 0.116 Hom.: 1072

Bravo AF: 0.0927

Asia WGS AF: 0.0770 AC: 266 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2084898; hg19: chr11-120026748;