rs2107195

Variant names:

• chr6-30170089-A-G
• rs2107195
• NM_033229.3:c.732-412A>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.732-412A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,066 control chromosomes in the GnomAD database, including 2,262 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 0.16 (2262 hom., cov: 31)
• Consequence: TRIM15 NM_033229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.72
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM15	NM_033229.3	c.732-412A>G		intron_variant	Intron 4 of 6	ENST00000376694.9	NP_150232.2
TRIM15	XM_011514987.2	c.417-412A>G		intron_variant	Intron 5 of 7		XP_011513289.1
TRIM15	XM_011514988.3	c.111-412A>G		intron_variant	Intron 2 of 4		XP_011513290.1
TRIM15	XM_047419503.1	c.718-412A>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.732-412A>G		intron_variant	Intron 4 of 6	1	NM_033229.3	ENSP00000365884.4
TRIM15	ENST00000619857.4	c.524+237A>G		intron_variant	Intron 5 of 7	5		ENSP00000484001.1
TRIM15	ENST00000433744.1	c.240-412A>G		intron_variant	Intron 2 of 4	3		ENSP00000398285.1
TRIM15	ENST00000477944.1	n.-224A>G		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24013 AN: 151948 Hom.: 2261 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.183

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.158 AC: 24048 AN: 152066 Hom.: 2262 Cov.: 31 AF XY: 0.156 AC XY: 11567 AN XY: 74334

African (AFR) AF: 0.253 AC: 10475 AN: 41424

American (AMR) AF: 0.148 AC: 2255 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3470

East Asian (EAS) AF: 0.0523 AC: 271 AN: 5178

South Asian (SAS) AF: 0.204 AC: 983 AN: 4816

European-Finnish (FIN) AF: 0.0360 AC: 382 AN: 10606

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8377 AN: 67982

Other (OTH) AF: 0.180 AC: 381 AN: 2112

Alfa AF: 0.149 Hom.: 1259

Bravo AF: 0.173

Asia WGS AF: 0.118 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.039
DANN	Benign	0.51
PhyloP100		-3.7
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: rs2107195; hg19: chr6-30137866;