chr6-30163572-T-C

Position:

• chr6-30163572-T-C

Variant summary

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

The NM_033229.3(TRIM15):​c.-113T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 1,300,994 control chromosomes in the GnomAD database, including 366,084 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 0.75 (43373 hom., cov: 31)
  • Exomes 𝑓: 0.74 (322711 hom.)
• Consequence: TRIM15 NM_033229.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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]

TRIM10 (HGNC:10072): (tripartite motif containing 10) 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. This protein localizes to cytoplasmic bodies. Studies in mice suggest that this protein plays a role in terminal differentiation of erythroid cells. Alternate splicing of this gene generates two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM15	NM_033229.3	c.-113T>C		5_prime_UTR_variant	1/7	ENST00000376694.9	NP_150232.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM15	ENST00000376694.9	c.-113T>C		5_prime_UTR_variant	1/7	1	NM_033229.3	ENSP00000365884.4
TRIM15	ENST00000619857.4	c.-320T>C		5_prime_UTR_variant	1/8	5		ENSP00000484001.1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113810 AN: 151854 Hom.: 43306 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.748

GnomAD4 exome AF: 0.744 AC: 855088 AN: 1149024 Hom.: 322711 Cov.: 16 AF XY: 0.742 AC XY: 420438 AN XY: 566516

Gnomad4 AFR exome AF: 0.900

Gnomad4 AMR exome AF: 0.828

Gnomad4 ASJ exome AF: 0.795

Gnomad4 EAS exome AF: 0.626

Gnomad4 SAS exome AF: 0.729

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.746

Gnomad4 OTH exome AF: 0.740

GnomAD4 genome AF: 0.750 AC: 113926 AN: 151970 Hom.: 43373 Cov.: 31 AF XY: 0.744 AC XY: 55255 AN XY: 74262

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.739

Alfa AF: 0.888 Hom.: 37893

Bravo AF: 0.924

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.65
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261536; hg19: chr6-30131349;