7-99891382-A-G

Variant names:

• chr7-99891382-A-G
• rs2572009
• NM_033091.3:c.*781T>C

Variant summary

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

The NM_033091.3(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 NM_033091.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033091.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM4	NM_033091.3	MANE Select	c.*781T>C		3_prime_UTR	Exon 6 of 6	NP_149082.1
	TRIM4	NM_033017.4		c.*781T>C		3_prime_UTR	Exon 7 of 7	NP_148977.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM4	ENST00000349062.7	TSL:1 MANE Select	c.*781T>C		3_prime_UTR	Exon 6 of 6	ENSP00000275736.4
	TRIM4	ENST00000355947.6	TSL:1	c.*781T>C		3_prime_UTR	Exon 7 of 7	ENSP00000348216.2
	TRIM4	ENST00000447480.5	TSL:3	c.544+11836T>C		intron	N/A	ENSP00000396229.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.883 AC: 36686 AN: 41536

American (AMR) AF: 0.515 AC: 7880 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1520 AN: 5174

South Asian (SAS) AF: 0.534 AC: 2578 AN: 4828

European-Finnish (FIN) AF: 0.597 AC: 6319 AN: 10576

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40097 AN: 67992

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.597 Hom.: 49833

Bravo AF: 0.649

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.30
PhyloP100		-0.77
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs2572009; hg19: chr7-99489005;