chr11-120156040-G-A

Variant names:

• chr11-120156040-G-A
• rs2084898
• ENST00000532833.1:c.-114-17895C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM29	ENST00000532833.1	c.-114-17895C>T		intron_variant	Intron 1 of 1	4		ENSP00000436567.1
TRIM29	ENST00000529040.1	c.-114-17895C>T		intron_variant	Intron 1 of 1	4		ENSP00000433084.1

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

African (AFR) AF: 0.0396 AC: 1645 AN: 41542

American (AMR) AF: 0.135 AC: 2069 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3470

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5184

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4826

European-Finnish (FIN) AF: 0.0912 AC: 965 AN: 10576

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8211 AN: 67992

Other (OTH) AF: 0.119 AC: 252 AN: 2116

Alfa AF: 0.111 Hom.: 2645

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2084898; hg19: chr11-120026748;