rs6905949

Variant names:

• chr6-30172748-T-C
• rs6905949
• NM_033229.3:c.*399T>C

Variant summary

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

The NM_033229.3(TRIM15):​c.*399T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 346,774 control chromosomes in the GnomAD database, including 6,393 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 0.17 (2562 hom., cov: 33)
  • Exomes 𝑓: 0.18 (3831 hom.)
• Consequence: TRIM15 NM_033229.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

Genes affected

TRIM15 (HGNC:16284): (tripartite motif containing 15) 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 the cytoplasm. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM15	NM_033229.3	c.*399T>C		downstream_gene_variant		ENST00000376694.9	NP_150232.2
TRIM15	XM_011514987.2	c.*399T>C		downstream_gene_variant			XP_011513289.1
TRIM15	XM_011514988.3	c.*399T>C		downstream_gene_variant			XP_011513290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM15	ENST00000376694.9	c.*399T>C		downstream_gene_variant		1	NM_033229.3	ENSP00000365884.4
TRIM15	ENST00000619857.4	c.*399T>C		downstream_gene_variant		5		ENSP00000484001.1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26618 AN: 152152 Hom.: 2553 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.205

GnomAD4 exome AF: 0.183 AC: 35646 AN: 194504 Hom.: 3831 AF XY: 0.195 AC XY: 20321 AN XY: 104456

Gnomad4 AFR exome AF: 0.175

Gnomad4 AMR exome AF: 0.129

Gnomad4 ASJ exome AF: 0.324

Gnomad4 EAS exome AF: 0.223

Gnomad4 SAS exome AF: 0.271

Gnomad4 FIN exome AF: 0.0897

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.175 AC: 26640 AN: 152270 Hom.: 2562 Cov.: 33 AF XY: 0.175 AC XY: 13012 AN XY: 74462

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.210

Alfa AF: 0.183 Hom.: 4149

Bravo AF: 0.182

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6905949; hg19: chr6-30140525;