6-30163572-T-C

Variant names:

• chr6-30163572-T-C
• rs9261536
• NM_033229.3:c.-113T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM15	NM_033229.3	c.-113T>C		5_prime_UTR_variant	Exon 1 of 7	ENST00000376694.9	NP_150232.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM15	ENST00000376694.9	c.-113T>C		5_prime_UTR_variant	Exon 1 of 7	1	NM_033229.3	ENSP00000365884.4
TRIM15	ENST00000619857.4	c.-320T>C		5_prime_UTR_variant	Exon 1 of 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

African (AFR) AF: 0.900 AC: 24658 AN: 27394

American (AMR) AF: 0.828 AC: 21083 AN: 25450

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 14634 AN: 18402

East Asian (EAS) AF: 0.626 AC: 22234 AN: 35516

South Asian (SAS) AF: 0.729 AC: 44900 AN: 61602

European-Finnish (FIN) AF: 0.624 AC: 20963 AN: 33592

Middle Eastern (MID) AF: 0.750 AC: 2595 AN: 3460

European-Non Finnish (NFE) AF: 0.746 AC: 667965 AN: 894914

Other (OTH) AF: 0.740 AC: 36056 AN: 48694

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

African (AFR) AF: 0.879 AC: 36492 AN: 41500

American (AMR) AF: 0.773 AC: 11818 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2726 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3344 AN: 5132

South Asian (SAS) AF: 0.692 AC: 3339 AN: 4822

European-Finnish (FIN) AF: 0.599 AC: 6312 AN: 10534

Middle Eastern (MID) AF: 0.767 AC: 221 AN: 288

European-Non Finnish (NFE) AF: 0.700 AC: 47525 AN: 67938

Other (OTH) AF: 0.739 AC: 1552 AN: 2100

Alfa AF: 0.893 Hom.: 147872

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
PhyloP100		-2.0
PromoterAI		0.090	Neutral
Mutation Taster		=299/1	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: rs9261536; hg19: chr6-30131349;