NM_152616.5:c.2086-2284T>C

Variant names:

• chr3-140698604-T-C
• rs79436609
• NM_152616.5:c.2086-2284T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_152616.5(TRIM42):​c.2086-2284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 151,716 control chromosomes in the GnomAD database, including 39 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 0.018 (39 hom., cov: 33)
• Consequence: TRIM42 NM_152616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 4 publications found

Genes affected

TRIM42 (HGNC:19014): (tripartite motif containing 42) This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, namely a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [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=-0.98).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.018 (2726/151716) while in subpopulation NFE AF = 0.0278 (1893/68018). AF 95% confidence interval is 0.0268. There are 39 homozygotes in GnomAd4. There are 1286 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 39 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152616.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM42	NM_152616.5	MANE Select	c.2086-2284T>C		intron	N/A	NP_689829.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM42	ENST00000286349.4	TSL:1 MANE Select	c.2086-2284T>C		intron	N/A	ENSP00000286349.3

Frequencies

GnomAD3 genomes AF: 0.0180 AC: 2728 AN: 151602 Hom.: 39 Cov.: 33

Gnomad AFR AF: 0.00531

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0167

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0250

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

GnomAD4 genome AF: 0.0180 AC: 2726 AN: 151716 Hom.: 39 Cov.: 33 AF XY: 0.0173 AC XY: 1286 AN XY: 74230

African (AFR) AF: 0.00529 AC: 217 AN: 40988

American (AMR) AF: 0.0167 AC: 255 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4834

European-Finnish (FIN) AF: 0.0197 AC: 209 AN: 10614

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0278 AC: 1893 AN: 68018

Other (OTH) AF: 0.0247 AC: 52 AN: 2106

Alfa AF: 0.0249 Hom.: 104

Bravo AF: 0.0170

Asia WGS AF: 0.00260 AC: 9 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.51
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism

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: rs79436609; hg19: chr3-140417446;