rs2527927

Positions:

• chr7-99879803-G-A

Variant summary

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

The ENST00000447480.5(TRIM4):​c.546-2752C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,800 control chromosomes in the GnomAD database, including 11,964 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 0.39 (11964 hom., cov: 31)
• Consequence: TRIM4 ENST00000447480.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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 (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM4	ENST00000447480.5	c.546-2752C>T		intron_variant		3		ENSP00000396229

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58618 AN: 151684 Hom.: 11961 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.386 AC: 58640 AN: 151800 Hom.: 11964 Cov.: 31 AF XY: 0.385 AC XY: 28560 AN XY: 74192

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.362

Alfa AF: 0.441 Hom.: 8611

Bravo AF: 0.367

Asia WGS AF: 0.401 AC: 1396 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	1.7
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2527927; hg19: chr7-99477426;