rs2130017

Variant names:

• chr11-89769208-C-A
• rs2130017
• XM_024448617.2:c.739-372G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.869 AC: 20934 AN: 24076

American (AMR) AF: 0.754 AC: 10550 AN: 13996

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2107 AN: 3170

East Asian (EAS) AF: 0.854 AC: 3747 AN: 4390

South Asian (SAS) AF: 0.758 AC: 2982 AN: 3932

European-Finnish (FIN) AF: 0.695 AC: 6580 AN: 9472

Middle Eastern (MID) AF: 0.735 AC: 197 AN: 268

European-Non Finnish (NFE) AF: 0.649 AC: 40975 AN: 63168

Other (OTH) AF: 0.694 AC: 1221 AN: 1760

Alfa AF: 0.829 Hom.: 10755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.40
DANN	Benign	0.49
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2130017; hg19: chr11-89502376;