rs1573298

chr6-30148383-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286633.2(TRIM40):c.*571G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 163,216 control chromosomes in the GnomAD database, including 4,550 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 0.23 (4302 hom., cov: 32)
  • Exomes 𝑓: 0.20 (248 hom.)
• Consequence: TRIM40 NM_001286633.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

Genes affected

TRIM40 (HGNC:18736): (tripartite motif containing 40) This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM40	NM_001286633.2	c.*571G>C		3_prime_UTR_variant	6/6	ENST00000396581.6
TRIM40	NM_138700.4	c.*571G>C		3_prime_UTR_variant	5/5
TRIM40	XM_011514306.2	c.*571G>C		3_prime_UTR_variant	7/7
TRIM40	XM_011514309.2	c.*602G>C		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM40	ENST00000396581.6	c.*571G>C		3_prime_UTR_variant	6/6	1	NM_001286633.2	P1
TRIM40	ENST00000307859.4	c.*571G>C		3_prime_UTR_variant	5/5	1
TRIM40	ENST00000376724.6	c.*571G>C		3_prime_UTR_variant	5/5	2		P1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34674 AN: 152018 Hom.: 4294 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.203

GnomAD4 exome AF: 0.205 AC: 2266 AN: 11078 Hom.: 248 Cov.: 0 AF XY: 0.204 AC XY: 1187 AN XY: 5832

Gnomad4 AFR exome AF: 0.0971

Gnomad4 AMR exome AF: 0.209

Gnomad4 ASJ exome AF: 0.0846

Gnomad4 EAS exome AF: 0.172

Gnomad4 SAS exome AF: 0.218

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.183

GnomAD4 genome AF: 0.228 AC: 34702 AN: 152138 Hom.: 4302 Cov.: 32 AF XY: 0.232 AC XY: 17227 AN XY: 74376

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.208

Alfa AF: 0.243 Hom.: 595

Bravo AF: 0.217

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.55

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: rs1573298; hg19: chr6-30116160;