chr3-140698604-T-C

Position:

• chr3-140698604-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 39 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM42	NM_152616.5	c.2086-2284T>C		intron_variant		ENST00000286349.4	NP_689829.3
TRIM42	XM_011512740.4	c.2086-1812T>C		intron_variant			XP_011511042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM42	ENST00000286349.4	c.2086-2284T>C		intron_variant		1	NM_152616.5	ENSP00000286349	P1

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

Gnomad4 AFR AF: 0.00529

Gnomad4 AMR AF: 0.0167

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.0197

Gnomad4 NFE AF: 0.0278

Gnomad4 OTH AF: 0.0247

Alfa AF: 0.0222 Hom.: 4

Bravo AF: 0.0170

Asia WGS AF: 0.00260 AC: 9 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.51

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: rs79436609; hg19: chr3-140417446;