rs1029239

Variant names:

• chr6-30170385-C-G
• rs1029239
• NM_033229.3:c.732-116C>G

Variant summary

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

The NM_033229.3(TRIM15):​c.732-116C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 622,646 control chromosomes in the GnomAD database, including 66,323 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 0.44 (15170 hom., cov: 31)
  • Exomes 𝑓: 0.46 (51153 hom.)
• Consequence: TRIM15 NM_033229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 22 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM15	NM_033229.3	c.732-116C>G		intron_variant	Intron 4 of 6	ENST00000376694.9	NP_150232.2
TRIM15	XM_011514987.2	c.417-116C>G		intron_variant	Intron 5 of 7		XP_011513289.1
TRIM15	XM_011514988.3	c.111-116C>G		intron_variant	Intron 2 of 4		XP_011513290.1
TRIM15	XM_047419503.1	c.718-116C>G		intron_variant	Intron 4 of 4		XP_047275459.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM15	ENST00000376694.9	c.732-116C>G		intron_variant	Intron 4 of 6	1	NM_033229.3	ENSP00000365884.4
TRIM15	ENST00000477944.1	n.73C>G		non_coding_transcript_exon_variant	Exon 1 of 2	3
TRIM15	ENST00000619857.4	c.525-116C>G		intron_variant	Intron 5 of 7	5		ENSP00000484001.1
TRIM15	ENST00000433744.1	c.240-116C>G		intron_variant	Intron 2 of 4	3		ENSP00000398285.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67231 AN: 151872 Hom.: 15147 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.459 AC: 216158 AN: 470656 Hom.: 51153 Cov.: 6 AF XY: 0.467 AC XY: 115941 AN XY: 248066

African (AFR) AF: 0.434 AC: 5645 AN: 13016

American (AMR) AF: 0.344 AC: 6201 AN: 18038

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 6945 AN: 13454

East Asian (EAS) AF: 0.465 AC: 14755 AN: 31746

South Asian (SAS) AF: 0.600 AC: 26406 AN: 44014

European-Finnish (FIN) AF: 0.398 AC: 14687 AN: 36910

Middle Eastern (MID) AF: 0.479 AC: 1707 AN: 3566

European-Non Finnish (NFE) AF: 0.449 AC: 127490 AN: 283708

Other (OTH) AF: 0.470 AC: 12322 AN: 26204

GnomAD4 genome AF: 0.443 AC: 67287 AN: 151990 Hom.: 15170 Cov.: 31 AF XY: 0.444 AC XY: 32950 AN XY: 74282

African (AFR) AF: 0.428 AC: 17709 AN: 41424

American (AMR) AF: 0.391 AC: 5981 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5156

South Asian (SAS) AF: 0.625 AC: 3010 AN: 4814

European-Finnish (FIN) AF: 0.412 AC: 4353 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30554 AN: 67966

Other (OTH) AF: 0.472 AC: 993 AN: 2104

Alfa AF: 0.458 Hom.: 9277

Bravo AF: 0.436

Asia WGS AF: 0.589 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.89
DANN	Benign	0.42
PhyloP100		-0.20
Mutation Taster		=100/0	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: rs1029239; hg19: chr6-30138162; COSMIC: COSV64990159;