rs2572010

Positions:

• chr7-99890920-C-T

Variant summary

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

The NM_033091.3(TRIM4):​c.*1243G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,146 control chromosomes in the GnomAD database, including 32,372 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 0.64 (32372 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: TRIM4 NM_033091.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

TRIM4 (HGNC:16275): (tripartite motif containing 4) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. Its function has not been identified. Alternatively spliced transcript variants that encode different isoforms have been described.[provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM4	NM_033091.3	c.*1243G>A		3_prime_UTR_variant	6/6	ENST00000349062.7	NP_149082.1
TRIM4	NM_033017.4	c.*1243G>A		3_prime_UTR_variant	7/7		NP_148977.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM4	ENST00000349062	c.*1243G>A		3_prime_UTR_variant	6/6	1	NM_033091.3	ENSP00000275736.4
TRIM4	ENST00000355947	c.*1243G>A		3_prime_UTR_variant	7/7	1		ENSP00000348216.2
TRIM4	ENST00000447480.5	c.544+12298G>A		intron_variant		3		ENSP00000396229.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96671 AN: 152028 Hom.: 32325 Cov.: 33

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.589

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.636 AC: 96775 AN: 152146 Hom.: 32372 Cov.: 33 AF XY: 0.628 AC XY: 46737 AN XY: 74364

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.583

Alfa AF: 0.600 Hom.: 10869

Bravo AF: 0.633

Asia WGS AF: 0.482 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs2572010; hg19: chr7-99488543;