rs2527927

Variant names:

• chr7-99879803-G-A
• rs2527927
• ENST00000447480.5:c.545-2752C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-99879803-G-A
• chr7-99879803-G-C
• chr7-99879803-G-T

Variant summary

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

The ENST00000447480.5(TRIM4):​c.545-2752C>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
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM4	ENST00000447480.5	c.545-2752C>T		intron_variant	Intron 5 of 5	3		ENSP00000396229.1

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

African (AFR) AF: 0.265 AC: 10951 AN: 41366

American (AMR) AF: 0.343 AC: 5237 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1516 AN: 5172

South Asian (SAS) AF: 0.425 AC: 2042 AN: 4808

European-Finnish (FIN) AF: 0.486 AC: 5097 AN: 10496

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31360 AN: 67934

Other (OTH) AF: 0.362 AC: 760 AN: 2102

Alfa AF: 0.431 Hom.: 28301

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2527927; hg19: chr7-99477426;