7-99891382-A-G

Position:

• chr7-99891382-A-G

Variant summary

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

The ENST00000349062.7(TRIM4):​c.*781T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,202 control chromosomes in the GnomAD database, including 33,945 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 0.65 (33943 hom., cov: 33)
  • Exomes 𝑓: 0.58 (2 hom.)
• Consequence: TRIM4 ENST00000349062.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM4	NM_033091.3	c.*781T>C		3_prime_UTR_variant	6/6	ENST00000349062.7	NP_149082.1
TRIM4	NM_033017.4	c.*781T>C		3_prime_UTR_variant	7/7		NP_148977.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM4	ENST00000349062.7	c.*781T>C		3_prime_UTR_variant	6/6	1	NM_033091.3	ENSP00000275736	P2
TRIM4	ENST00000355947.6	c.*781T>C		3_prime_UTR_variant	7/7	1		ENSP00000348216	A2
TRIM4	ENST00000447480.5	c.545+11836T>C		intron_variant		3		ENSP00000396229

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98580 AN: 152072 Hom.: 33891 Cov.: 33

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.600

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.648 AC: 98692 AN: 152190 Hom.: 33943 Cov.: 33 AF XY: 0.641 AC XY: 47697 AN XY: 74394

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.597

Alfa AF: 0.588 Hom.: 34495

Bravo AF: 0.649

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.30
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2572009; hg19: chr7-99489005;