rs10489419

Variant names:

• chr1-114406147-T-G
• rs10489419
• NM_015906.4:c.2419-388A>C

Variant summary

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

The NM_015906.4(TRIM33):​c.2419-388A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 152,260 control chromosomes in the GnomAD database, including 154 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 0.043 (154 hom., cov: 32)
• Consequence: TRIM33 NM_015906.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 2 publications found

Genes affected

TRIM33 (HGNC:16290): (tripartite motif containing 33) The protein encoded by this gene is thought to be a transcriptional corepressor. However, molecules that interact with this protein have not yet been identified. The protein is a member of the tripartite motif family. This motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. Three alternatively spliced transcript variants for this gene have been described, however, the full-length nature of one variant has not been determined. [provided by RefSeq, Jul 2008]

TRIM33 Gene-Disease associations (from GenCC):

• developmental dysplasia of the hip

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM33	NM_015906.4	c.2419-388A>C		intron_variant	Intron 14 of 19	ENST00000358465.7	NP_056990.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM33	ENST00000358465.7	c.2419-388A>C		intron_variant	Intron 14 of 19	1	NM_015906.4	ENSP00000351250.2
TRIM33	ENST00000369543.6	c.2419-388A>C		intron_variant	Intron 14 of 18	1		ENSP00000358556.2
TRIM33	ENST00000448034.5	c.1699-388A>C		intron_variant	Intron 12 of 17	5		ENSP00000402333.1
TRIM33	ENST00000476908.1	n.28-388A>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6594 AN: 152142 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0627

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0532

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

GnomAD4 genome AF: 0.0434 AC: 6601 AN: 152260 Hom.: 154 Cov.: 32 AF XY: 0.0429 AC XY: 3197 AN XY: 74454

African (AFR) AF: 0.0628 AC: 2607 AN: 41536

American (AMR) AF: 0.0371 AC: 567 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0634 AC: 306 AN: 4824

European-Finnish (FIN) AF: 0.0191 AC: 203 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0381 AC: 2593 AN: 68012

Other (OTH) AF: 0.0527 AC: 111 AN: 2108

Alfa AF: 0.0415 Hom.: 109

Bravo AF: 0.0446

Asia WGS AF: 0.0490 AC: 169 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.59
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10489419; hg19: chr1-114948769;