rs11228904

Variant names:

• chr11-55262739-G-A
• rs11228904
• NM_024114.5:c.44+428G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024114.5(TRIM48):​c.44+428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,922 control chromosomes in the GnomAD database, including 1,066 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 0.11 (1066 hom., cov: 32)
• Consequence: TRIM48 NM_024114.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.673
• Publications: 2 publications found

Genes affected

TRIM48 (HGNC:19021): (tripartite motif containing 48) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in innate immune response; protein ubiquitination; and regulation of gene expression. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM48	NM_024114.5	c.44+428G>A		intron_variant	Intron 1 of 5	ENST00000417545.5	NP_077019.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM48	ENST00000417545.5	c.44+428G>A		intron_variant	Intron 1 of 5	1	NM_024114.5	ENSP00000402414.2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16508 AN: 151802 Hom.: 1064 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16513 AN: 151922 Hom.: 1066 Cov.: 32 AF XY: 0.111 AC XY: 8237 AN XY: 74240

African (AFR) AF: 0.0906 AC: 3757 AN: 41464

American (AMR) AF: 0.121 AC: 1843 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5158

South Asian (SAS) AF: 0.281 AC: 1356 AN: 4820

European-Finnish (FIN) AF: 0.0528 AC: 557 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7057 AN: 67946

Other (OTH) AF: 0.108 AC: 227 AN: 2104

Alfa AF: 0.0985 Hom.: 112

Bravo AF: 0.110

Asia WGS AF: 0.258 AC: 890 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.074
PhyloP100		0.67
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11228904; hg19: chr11-55030215;