7-99890920-C-T

Variant names:

• chr7-99890920-C-T
• rs2572010
• NM_033091.3:c.*1243G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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.*1243G>A		3_prime_UTR	Exon 6 of 6	NP_149082.1
	TRIM4	NM_033017.4		c.*1243G>A		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.*1243G>A		3_prime_UTR	Exon 6 of 6	ENSP00000275736.4
	TRIM4	ENST00000355947.6	TSL:1	c.*1243G>A		3_prime_UTR	Exon 7 of 7	ENSP00000348216.2
	TRIM4	ENST00000447480.5	TSL:3	c.544+12298G>A		intron	N/A	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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.845 AC: 35079 AN: 41536

American (AMR) AF: 0.500 AC: 7645 AN: 15288

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

East Asian (EAS) AF: 0.295 AC: 1528 AN: 5186

South Asian (SAS) AF: 0.530 AC: 2558 AN: 4822

European-Finnish (FIN) AF: 0.599 AC: 6315 AN: 10550

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.589 AC: 40068 AN: 67978

Other (OTH) AF: 0.583 AC: 1232 AN: 2112

Alfa AF: 0.605 Hom.: 13209

Bravo AF: 0.633

Asia WGS AF: 0.482 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.70
PhyloP100		-0.81
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: rs2572010; hg19: chr7-99488543;