rs2444240

chr11-120169734-T-G

Variant summary

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

The NR_159965.1(LOC107984399):n.173-37T>G variant causes a intron, non coding transcript 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: LOC107984399 NR_159965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

(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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984399	NR_159965.1	n.173-37T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000319763.1	n.173-37T>G		intron_variant, non_coding_transcript_variant		1
	ENST00000530303.5	n.173-37T>G		intron_variant, non_coding_transcript_variant		1
TRIM29	ENST00000529040.1	c.-115+15476A>C		intron_variant		4
TRIM29	ENST00000532833.1	c.-115+15516A>C		intron_variant		4

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

Gnomad4 AFR exome AF: 0.367

Gnomad4 AMR exome AF: 0.468

Gnomad4 ASJ exome AF: 0.427

Gnomad4 EAS exome AF: 0.232

Gnomad4 SAS exome AF: 0.449

Gnomad4 FIN exome AF: 0.461

Gnomad4 NFE exome AF: 0.428

Gnomad4 OTH exome AF: 0.421

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.403

Alfa AF: 0.422 Hom.: 6417

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
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2444240; hg19: chr11-120040442;