rs2130017

Positions:

• chr11-89769208-C-A
• chr11-89769208-C-G
• chr11-89769208-C-T

Variant summary

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

The XM_024448617.2(TRIM49):​c.739-372G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 125,066 control chromosomes in the GnomAD database, including 35,319 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 0.72 (35319 hom., cov: 21)
• Consequence: TRIM49 XM_024448617.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

TRIM49 (HGNC:13431): (tripartite motif containing 49) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. This gene has been found to be preferentially expressed in testis. Related pseudogenes and gene duplicates have also been identified on chromosome 11. [provided by RefSeq, Aug 2010]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM49	XM_024448617.2	c.739-372G>T		intron_variant			XP_024304385.1
		n.89769208C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.719 AC: 89861 AN: 125022 Hom.: 35289 Cov.: 21

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.719 AC: 89915 AN: 125066 Hom.: 35319 Cov.: 21 AF XY: 0.722 AC XY: 43891 AN XY: 60828

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.694

Alfa AF: 0.739 Hom.: 4937

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2130017; hg19: chr11-89502376;